Soybean Cultivar 7904162

ABSTRACT

A soybean cultivar designated 7904162 is disclosed. The invention relates to the seeds of soybean cultivar 7904162, to the plants of soybean 7904162, to plant parts of soybean cultivar 7904162 and to methods for producing a soybean plant produced by crossing soybean cultivar 7904162 with itself or with another soybean variety. The invention also relates to methods for producing a soybean plant containing in its genetic material one or more transgenes and to the transgenic soybean plants and plant parts produced by those methods. This invention also relates to soybean cultivars or breeding cultivars and plant parts derived from soybean variety 7904162, to methods for producing other soybean cultivars, lines or plant parts derived from soybean cultivar 7904162 and to the soybean plants, varieties, and their parts derived from use of those methods. The invention further relates to hybrid soybean seeds, plants and plant parts produced by crossing the cultivar 7904162 with another soybean cultivar.

BACKGROUND OF THE INVENTION

The present invention relates to a new and distinctive soybean cultivar,designated 7904162. All publications cited in this application areherein incorporated by reference.

There are numerous steps in the development of any novel, desirableplant germplasm. Plant breeding begins with the analysis and definitionof problems and weaknesses of the current germplasm, the establishmentof program goals, and the definition of specific breeding objectives.The next step is selection of germplasm that possesses the traits tomeet the program goals. The goal is to combine in a single variety animproved combination of desirable traits from the parental germplasm.These important traits may include higher seed yield, resistance todiseases and insects, better stems and roots, tolerance to drought andheat, and better agronomic quality.

Choice of breeding or selection methods depends on the mode of plantreproduction, the heritability of the trait(s) being improved, and thetype of cultivar used commercially (e.g., F₁ hybrid cultivar, purelinecultivar, etc.). For highly heritable traits, a choice of superiorindividual plants evaluated at a single location will be effective,whereas for traits with low heritability, selection should be based onmean values obtained from replicated evaluations of families of relatedplants. Popular selection methods commonly include pedigree selection,modified pedigree selection, mass selection, and recurrent selection.

The complexity of inheritance influences choice of the breeding method.Backcross breeding is used to transfer one or a few favorable genes fora highly heritable trait into a desirable cultivar. This approach hasbeen used extensively for breeding disease-resistant cultivars. Variousrecurrent selection techniques are used to improve quantitativelyinherited traits controlled by numerous genes. The use of recurrentselection in self-pollinating crops depends on the ease of pollination,the frequency of successful hybrids from each pollination and the numberof hybrid offspring from each successful cross.

Each breeding program should include a periodic, objective evaluation ofthe efficiency of the breeding procedure. Evaluation criteria varydepending on the goal and objectives, but should include gain fromselection per year based on comparisons to an appropriate standard,overall value of the advanced breeding lines, and number of successfulcultivars produced per unit of input (e.g., per year, per dollarexpended, etc.).

Promising advanced breeding lines are thoroughly tested and compared toappropriate standards in environments representative of the commercialtarget area(s) for three or more years. The best lines are candidatesfor new commercial cultivars; those still deficient in a few traits maybe used as parents to produce new populations for further selection.

These processes, which lead to the final step of marketing anddistribution, usually take from eight to twelve years from the time thefirst cross is made. Therefore, development of new cultivars is atime-consuming process that requires precise forward planning, efficientuse of resources, and a minimum of changes in direction.

A most difficult task is the identification of individuals that aregenetically superior, because for most traits the true genotypic valueis masked by other confounding plant traits or environmental factors.One method of identifying a superior plant is to observe its performancerelative to other experimental plants and to a widely grown standardcultivar. If a single observation is inconclusive, replicatedobservations provide a better estimate of its genetic worth.

The goal of soybean plant breeding is to develop new, unique andsuperior soybean cultivars and hybrids. The breeder initially selectsand crosses two or more parental lines, followed by repeated selfing andselection, producing many new genetic combinations. The breeder cantheoretically generate billions of different genetic combinations viacrossing, selfing and mutations. The breeder has no direct control atthe cellular level. Therefore, two breeders will never develop the sameline, or even very similar lines, having the same soybean traits.

Each year, the plant breeder selects the germplasm to advance to thenext generation. This germplasm is grown under unique and differentgeographical, climatic and soil conditions and further selections arethen made during and at the end of the growing season. The cultivarsthat are developed are unpredictable because the breeder's selectionoccurs in unique environments with no control at the DNA level (usingconventional breeding procedures), and with millions of differentpossible genetic combinations being generated. A breeder of ordinaryskill in the art cannot predict the final resulting lines he develops,except possibly in a very gross and general fashion. The same breedercannot produce the same cultivar twice by using the same originalparents and the same selection techniques. This unpredictability resultsin the expenditure of large amounts of research monies to developsuperior new soybean cultivars.

The development of new soybean cultivars requires the development andselection of soybean varieties, the crossing of these varieties andselection of superior hybrid crosses. The hybrid seed is produced bymanual crosses between selected male-fertile parents or by using malesterility systems. These hybrids are selected for certain single genetraits such as pod color, flower color, pubescence color or herbicideresistance which indicate that the seed is truly a hybrid. Additionaldata on parental lines, as well as the phenotype of the hybrid,influence the breeder's decision whether to continue with the specifichybrid cross.

Pedigree breeding and recurrent selection breeding methods are used todevelop cultivars from breeding populations. Breeding programs combinedesirable traits from two or more cultivars or various broad-basedsources into breeding pools from which cultivars are developed byselfing and selection of desired phenotypes. The new cultivars areevaluated to determine which have commercial potential.

Pedigree breeding is used commonly for the improvement ofself-pollinating crops. Two parents that possess favorable,complementary traits are crossed to produce an F₁. An F₂ population isproduced by selfing one or several F₁s. Selection of the bestindividuals may begin in the F₂ population; then, beginning in the F₃,the best individuals in the best families are selected. Replicatedtesting of families can begin in the F₄ generation to improve theeffectiveness of selection for traits with low heritability. At anadvanced stage of inbreeding (i.e., F₆ and F₇), the best lines ormixtures of phenotypically similar lines are tested for potentialrelease as new cultivars.

Mass and recurrent selections can be used to improve populations ofeither self- or cross-pollinating crops. A genetically variablepopulation of heterozygous individuals is either identified, or created,by intercrossing several different parents. The best plants are selectedbased on individual superiority, outstanding progeny, or excellentcombining ability. The selected plants are intercrossed to produce a newpopulation in which further cycles of selection are continued.

Backcross breeding has been used to transfer genes for a simplyinherited, highly heritable trait into a desirable homozygous cultivaror inbred line which is the recurrent parent. The source of the trait tobe transferred is called the donor parent. After the initial cross,individuals possessing the phenotype of the donor parent are selectedand repeatedly crossed (backcrossed) to the recurrent parent. Theresulting plant is expected to have the attributes of the recurrentparent (e.g., cultivar) and the desirable trait transferred from thedonor parent.

The single-seed descent procedure in the strict sense refers to plantinga segregating population, harvesting a sample of one seed per plant, andusing the one-seed sample to plant the next generation. When thepopulation has been advanced from the F₂ to the desired level ofinbreeding, the plants from which lines are derived will each trace todifferent F₂ individuals. The number of plants in a population declineseach generation due to failure of some seeds to germinate or some plantsto produce at least one seed. As a result, not all of the F₂ plantsoriginally sampled in the population will be represented by a progenywhen generation advance is completed.

In a multiple-seed procedure, soybean breeders commonly harvest one ormore pods from each plant in a population and thresh them together toform a bulk. Part of the bulk is used to plant the next generation andpart is put in reserve. The procedure has been referred to as modifiedsingle-seed descent or the pod-bulk technique.

The multiple-seed procedure has been used to save labor at harvest. Itis considerably faster to thresh pods with a machine than to remove oneseed from each by hand for the single-seed procedure. The multiple-seedprocedure also makes it possible to plant the same number of seeds of apopulation each generation of inbreeding. Enough seeds are harvested tomake up for those plants that did not germinate or produce seed.

In addition to phenotypic observations, the genotype of a plant can alsobe examined. There are many laboratory-based techniques available forthe analysis, comparison and characterization of plant genotype; amongthese are Isozyme Electrophoresis, Restriction Fragment LengthPolymorphisms (RFLPs), Randomly Amplified Polymorphic DNAs (RAPDs),Arbitrarily Primed Polymerase Chain Reaction (AP-PCR), DNA AmplificationFingerprinting (DAF), Sequence Characterized Amplified Regions (SCARs),Amplified Fragment Length polymorphisms (AFLPs), Simple Sequence Repeats(SSRs—which are also referred to as Microsatellites), and SingleNucleotide Polymorphisms (SNPs).

Proper testing should detect any major faults and establish the level ofsuperiority or improvement over current cultivars. In addition toshowing superior performance, there must be a demand for a new cultivarthat is compatible with industry standards or which creates a newmarket. The introduction of a new cultivar will incur additional coststo the seed producer, the grower, processor and consumer for specialadvertising and marketing, altered seed and commercial productionpractices, and new product utilization. The testing preceding release ofa new cultivar should take into consideration research and developmentcosts as well as technical superiority of the final cultivar. Forseed-propagated cultivars, it must be feasible to produce seed easilyand economically.

Soybean, Glycine max (L), is an important and valuable field crop. Thus,a continuing goal of soybean plant breeders is to develop stable, highyielding soybean cultivars that are agronomically sound. The reasons forthis goal are obviously to maximize the amount of grain produced on theland used and to supply food for both animals and humans. To accomplishthis goal, the soybean breeder must select and develop soybean plantsthat have traits that result in superior cultivars.

The foregoing examples of the related art and limitations relatedtherewith are intended to be illustrative and not exclusive. Otherlimitations of the related art will become apparent to those of skill inthe art upon a reading of the specification.

SUMMARY OF THE INVENTION

The following embodiments and aspects thereof are described inconjunction with systems, tools and methods which are meant to beexemplary, not limiting in scope. In various embodiments, one or more ofthe above-described problems have been reduced or eliminated, whileother embodiments are directed to other improvements.

According to the invention, there is provided a new soybean cultivardesignated 7904162. This invention thus relates to the seeds of soybeancultivar 7904162, to the plants of soybean cultivar 7904162 and tomethods for producing a soybean plant produced by crossing the soybeancultivar 7904162 with itself or another soybean cultivar, and thecreation of variants by mutagenesis or transformation of soybeancultivar 7904162.

Thus, any such methods using the soybean cultivar 7904162 are part ofthis invention: selfing, backcrosses, hybrid production, crosses topopulations, and the like. All plants produced using soybean cultivar7904162 as at least one parent are within the scope of this invention.Advantageously, the soybean cultivar could be used in crosses withother, different, soybean plants to produce first generation (F₁)soybean hybrid seeds and plants with superior characteristics.

In another aspect, the present invention provides for single or multiplegene converted plants of soybean cultivar 7904162. The transferredgene(s) may preferably be a dominant or recessive allele. Preferably,the transferred gene(s) will confer such traits as herbicide resistance,insect resistance, resistance for bacterial, fungal, or viral disease,male fertility, male sterility, enhanced nutritional quality, modifiedfatty acid metabolism, modified carbohydrate metabolism, modified seedyield, modified oil percent, modified protein percent, modified lodgingresistance, modified shattering, modified iron-deficiency chlorosis andindustrial usage. The gene may be a naturally occurring soybean gene ora transgene introduced through genetic engineering techniques.

In another aspect, the present invention provides regenerable cells foruse in tissue culture of soybean plant 7904162. The tissue culture willpreferably be capable of regenerating plants having all thephysiological and morphological characteristics of the foregoing soybeanplant, and of regenerating plants having substantially the same genotypeas the foregoing soybean plant. Preferably, the regenerable cells insuch tissue cultures will be embryos, protoplasts, meristematic cells,callus, pollen, leaves, anthers, cotyledons, hypocotyl, pistils, roots,root tips, flowers, seeds, petiole, pods or stems. Still further, thepresent invention provides soybean plants regenerated from the tissuecultures of the invention.

In addition to the exemplary aspects and embodiments described above,further aspects and embodiments will become apparent by study of thefollowing descriptions.

DEFINITIONS

In the description and tables that follow, a number of terms are used.In order to provide a clear and consistent understanding of thespecification and claims, including the scope to be given such terms,the following definitions are provided:

Allele. An allele is any of one or more alternative forms of a genewhich relate to one trait or characteristic. In a diploid cell ororganism, the two alleles of a given gene occupy corresponding loci on apair of homologous chromosomes.

Backcrossing. Backcrossing is a process in which a breeder repeatedlycrosses hybrid progeny back to one of the parents, for example, a firstgeneration hybrid F₁ with one of the parental genotypes of the F₁hybrid.

Alter. The utilization of up-regulation, down-regulation, or genesilencing.

Brown Stem Rot. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. The score is based on leaf symptoms ofyellowing and necrosis caused by brown stem rot. Visual scores rangefrom a score of 9, which indicates no symptoms, to a score of 1 whichindicates severe symptoms of leaf yellowing and necrosis.

Cell. Cell as used herein includes a plant cell, whether isolated, intissue culture or incorporated in a plant or plant part.

Cotyledon. A cotyledon is a type of seed leaf. The cotyledon containsthe food storage tissues of the seed.

Embryo. The embryo is the small plant contained within a mature seed.

Emergence. This score indicates the ability of the seed to emerge whenplanted 3″ deep in sand at a controlled temperature of 25° C. The numberof plants that emerge each day are counted. Based on this data, eachgenotype is given a 1 to 9 score based on its rate of emergence andpercent of emergence. A score of 9 indicates an excellent rate andpercent of emergence, an intermediate score of 5 indicates averageratings and a 1 score indicates a very poor rate and percent ofemergence.

F₃. The “F₃” symbol denotes a generation resulting from the selfing ofthe F₂ generation along with selection for type and rogueing ofoff-types. The “F” number is a term commonly used in genetics, anddesignates the number of the filial generation.

The “F₃” generation denotes the offspring resulting from the selfing orself mating of members of the generation having the next lower “F”number, viz. the F₂ generation.

Gene Silencing. The interruption or suppression of the expression of agene at the level of transcription or translation.

Genotype. Refers to the genetic constitution of a cell or organism.

Hilum. This refers to the scar left on the seed that marks the placewhere the seed was attached to the pod prior to the seed beingharvested.

Hypocotyl. A hypocotyl is the portion of an embryo or seedling betweenthe cotyledons and the root. Therefore, it can be considered atransition zone between shoot and root.

Iron Deficiency Chlorosis. Iron deficiency chlorosis (IDC) is ayellowing of the leaves caused by a lack of iron in the soybean plant.Iron is essential in the formation of chlorophyll, which gives plantstheir green color. In high pH soils iron becomes insoluble and cannot beabsorbed by plant roots. Soybean cultivars differ in their geneticability to utilize the available iron. A score of 9 means no stunting ofthe plants or yellowing of the leaves and a score of 1 indicates theplants are dead or dying caused by iron deficiency, a score of 5 meansplants have intermediate health with some leaf yellowing.

Linkage. Refers to a phenomenon wherein alleles on the same chromosometend to segregate together more often than expected by chance if theirtransmission was independent.

Linkage Disequilibrium. Refers to a phenomenon wherein alleles tend toremain together in linkage groups when segregating from parents tooffspring, with a greater frequency than expected from their individualfrequencies.

Linoleic Acid Percent. Linoleic acid is one of the five most abundantfatty acids in soybean seeds. It is measured by gas chromatography andis reported as a percent of the total oil content.

Locus. A locus confers one or more traits such as, for example, malesterility, herbicide tolerance, insect resistance, disease resistance,waxy starch, modified fatty acid metabolism, modified phytic acidmetabolism, modified carbohydrate metabolism and modified proteinmetabolism. The trait may be, for example, conferred by a naturallyoccurring gene introduced into the genome of the variety bybackcrossing, a natural or induced mutation, or a transgene introducedthrough genetic transformation techniques. A locus may comprise one ormore alleles integrated at a single chromosomal location.

Lodging Resistance. Lodging is rated on a scale of 1 to 9. A score of 9indicates erect plants. A score of 5 indicates plants are leaning at a45° angle in relation to the ground and a score of 1 indicates plantsare lying on the ground.

Maturity Date. Plants are considered mature when 95% of the pods havereached their mature color. The number of days are calculated eitherfrom August 31 or from the planting date.

Maturity Group. This refers to an agreed-on industry division of groupsof varieties based on zones in which they are adapted, primarilyaccording to day length or latitude. They consist of very long daylength varieties (Groups 000, 00, 0), and extend to very short daylength varieties (Groups VII, VIII, IX, X).

Relative Maturity (RM). The term relative maturity is a numerical valuethat is assigned to a soybean variety based on comparisons with thematurity values of other varieties. The number preceding the decimalpoint in the RM refers to the maturity group. The number following thedecimal point refers to the relative earliness or lateness within eachmaturity group. For example, a 3.0 is an early group III variety, whilea 3.9 is a late group III variety.

Oil or oil percent. Soybean seeds contain a considerable amount of oil.Oil is measured by NIR spectrophotometry, and is reported as apercentage basis.

Oleic Acid Percent. Oleic acid is one of the five most abundant fattyacids in soybean seeds. It is measured by gas chromatography and isreported as a percent of the total oil content.

Palmitic Acid Percent. Palmitic acid is one of the five most abundantfatty acids in soybean seeds. It is measured by gas chromatography andis reported as a percent of the total oil content.

Pedigree Distance. Relationship among generations based on theirancestral links as evidenced in pedigrees. May be measured by thedistance of the pedigree from a given starting point in the ancestry.

Percent Identity. Percent identity as used herein refers to thecomparison of the homozygous alleles of two soybean varieties. Percentidentity is determined by comparing a statistically significant numberof the homozygous alleles of two developed varieties. For example, apercent identity of 90% between soybean variety 1 and soybean variety 2means that the two varieties have the same allele at 90% of their loci.

Percent Similarity. Percent similarity as used herein refers to thecomparison of the homozygous alleles of a soybean variety such as7904162 with another plant, and if the homozygous allele of 7904162matches at least one of the alleles from the other plant then they arescored as similar. Percent similarity is determined by comparing astatistically significant number of loci and recording the number ofloci with similar alleles as a percentage. A percent similarity of 90%between 7904162 and another plant means that 7904162 matches at leastone of the alleles of the other plant at 90% of the loci.

Phytophthora Tolerance. Tolerance to Phytophthora root rot is rated on ascale of 1 to 9, with a score of 9 being the best or highest toleranceranging down to a score of 1 which indicates the plants have notolerance to Phytophthora.

Phenotypic Score. The Phenotypic Score is a visual rating of generalappearance of the variety. All visual traits are considered in the scoreincluding healthiness, standability, appearance and freedom of disease.Ratings are scored from 1 being poor to 9 being excellent.

Plant. As used herein, the term “plant” includes reference to animmature or mature whole plant, including a plant from which seed orgrain or anthers have been removed. Seed or embryo that will produce theplant is also considered to be the plant.

Plant Height. Plant height is taken from the top of the soil to the topnode of the plant and is measured in centimeters.

Plant Parts. As used herein, the term “plant parts” (or a soybean plant,or a part thereof) includes protoplasts, leaves, stems, roots, roottips, anthers, seed, grain, embryo, pollen, ovules, cotyledon,hypocotyl, pod, flower, shoot, tissue, petiole, cells, meristematiccells and the like.

Pod. This refers to the fruit of a soybean plant. It consists of thehull or shell (pericarp) and the soybean seeds.

Protein Percent. Soybean seeds contain a considerable amount of protein.Protein is generally measured by NIR spectrophotometry and is reportedon an as is percentage basis.

Pubescence. This refers to a covering of very fine hairs closelyarranged on the leaves, stems and pods of the soybean plant.

Quantitative Trait Loci (QTL). Quantitative trait loci (QTL) refer togenetic loci that control to some degree numerically representabletraits that are usually continuously distributed.

Regeneration. Regeneration refers to the development of a plant fromtissue culture.

Seed Protein Peroxidase Activity. Seed protein peroxidase activityrefers to a chemical taxonomic technique to separate cultivars based onthe presence or absence of the peroxidase enzyme in the seed coat. Thereare two types of soybean cultivars, those having high peroxidaseactivity (dark red color) and those having low peroxidase activity (nocolor).

Seed Yield (Bushels/Acre). The yield in bushels/acre is the actual yieldof the grain at harvest.

Seeds per Pound. Soybean seeds vary in seed size, therefore, the numberof seeds required to make up one pound also varies. The number of seedsper pound affect the pounds of seed required to plant a given area andcan also impact end uses.

Shattering. The amount of pod dehiscence prior to harvest. Poddehiscence involves seeds falling from the pods to the soil. This is avisual score from 1 to 9 comparing all genotypes within a given test. Ascore of 9 means pods have not opened and no seeds have fallen out. Ascore of 5 indicates approximately 50% of the pods have opened, withseeds falling to the ground and a score of 1 indicates 100% of the podsare opened.

Single Gene Converted (Conversion). Single gene converted (conversion)plants refers to plants which are developed by a plant breedingtechnique called backcrossing wherein essentially all of the desiredmorphological and physiological characteristics of a variety arerecovered in addition to the single gene transferred into the varietyvia the backcrossing technique or via genetic engineering.

DETAILED DESCRIPTION OF THE INVENTION

Soybean cultivar 7904162 is a mid-maturity group I variety withresistance to glyphosate herbicides, including ROUNDUP herbicide.Additionally, soybean cultivar 7904162 contains the Rps 1k geneconferring resistance to Phytophthora Root Rot and the rhg1 geneconferring resistance to Soybean Cyst Nematode. Soybean cultivar 7904162has very high yield potential when compared to lines of similar maturityand has excellent agronomic characteristics including lodgingresistance.

Some of the selection criteria used for various generations include:seed yield, lodging resistance, emergence, disease tolerance, maturity,late season plant intactness, plant height and shattering resistance.

The cultivar has shown uniformity and stability, as described in thefollowing variety description information. It has been self-pollinated asufficient number of generations with careful attention to uniformity ofplant type. The line has been increased with continued observation foruniformity.

Soybean cultivar 7904162 has the following morphologic and othercharacteristics (based primarily on data collected at AdeI, Iowa).

TABLE 1 VARIETY DESCRIPTION INFORMATION Seed Coat Color (Mature Seed):Yellow Seed Coat Luster (Mature Hand Shelled Dull Seed): Cotyledon Color(Mature Seed): Yellow Leaflet Shape: Ovate Growth Habit: IndeterminateFlower Color: Purple Hilum Color (Mature Seed): Imperfect Black PlantPubescence Color: Gray Pod Wall Color: Tan Maturity Group: I RelativeMaturity: 1.4 Plant Lodging Score: 8.0 Plant Height (cm): 86 Seed Size(# Seeds/lb.): 2700 Seed Content: % Protein: 38.7 % Oil: 23.6Physiological Responses: ROUNDUP herbicide resistance to glyphosateherbicides Disease resistance: Phytophthora Root Rot - Rps 1k SoybeanCyst Nematode - rhg 1

This invention is also directed to methods for producing a soybean plantby crossing a first parent soybean plant with a second parent soybeanplant, wherein the first or second soybean plant is the soybean plantfrom cultivar 7904162. Further, both first and second parent soybeanplants may be from cultivar 7904162. Therefore, any methods usingsoybean cultivar 7904162 are part of this invention: selfing,backcrosses, hybrid breeding, and crosses to populations. Any plantsproduced using soybean cultivar 7904162 as at least one parent arewithin the scope of this invention.

Additional methods include, but are not limited to, expression vectorsintroduced into plant tissues using a direct gene transfer method suchas microprojectile-mediated delivery, DNA injection, electroporation andthe like. More preferably, expression vectors are introduced into planttissues by using either microprojectile-mediated delivery with abiolistic device or by using Agrobacterium-mediated transformation.Transformant plants obtained with the protoplasm of the invention areintended to be within the scope of this invention.

Soybean cultivar 7904162 is similar to soybean cultivar DAK2301AOR.While similar to soybean cultivar DAK2301AOR, there are significantdifferences including: soybean cultivar 7904162 has a relative maturityof 1.4, while soybean cultivar DAK2301AOR has a relative maturity of2.3.

FURTHER EMBODIMENTS OF THE INVENTION

The advent of new molecular biological techniques has allowed theisolation and characterization of genetic elements with specificfunctions, such as encoding specific protein products. Scientists in thefield of plant biology developed a strong interest in engineering thegenome of plants to contain and express foreign genetic elements, oradditional, or modified versions of native or endogenous geneticelements in order to alter the traits of a plant in a specific manner.Any DNA sequences, whether from a different species or from the samespecies, which are inserted into the genome using transformation arereferred to herein collectively as “transgenes”. In some embodiments ofthe invention, a transgenic variant of 7904162 may contain at least onetransgene but could contain at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10and/or no more than 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2.Over the last fifteen to twenty years several methods for producingtransgenic plants have been developed, and the present invention alsorelates to transgenic variants of the claimed soybean variety 7904162.

One embodiment of the invention is a process for producing soybeanvariety 7904162 further comprising a desired trait, said processcomprising transforming a soybean plant of variety 7904162 with atransgene that confers a desired trait. Another embodiment is theproduct produced by this process. In one embodiment the desired traitmay be one or more of herbicide resistance, insect resistance, diseaseresistance, decreased phytate, or modified fatty acid or carbohydratemetabolism. The specific gene may be any known in the art or listedherein, including; a polynucleotide conferring resistance toimidazolinone, sulfonylurea, glyphosate, glufosinate, triazine,benzonitrile, cyclohexanedione, phenoxy proprionic acid andL-phosphinothricin; a polynucleotide encoding a Bacillus thuringiensispolypeptide, a polynucleotide encoding phytase, FAD-2, FAD-3, galactinolsynthase or a raffinose synthetic enzyme; or a polynucleotide conferringresistance to soybean cyst nematode, brown stem rot, Phytophthora rootrot, soybean mosaic virus or sudden death syndrome.

Numerous methods for plant transformation have been developed, includingbiological and physical plant transformation protocols. See, forexample, Miki et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, Glick,B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages67-88 and Armstrong, “The First Decade of Maize Transformation: A Reviewand Future Perspective” (Maydica 44:101-109, 1999). In addition,expression vectors and in vitro culture methods for plant cell or tissuetransformation and regeneration of plants are available. See, forexample, Gruber et al., “Vectors for Plant Transformation” in Methods inPlant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J.E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages 89-119.

A genetic trait which has been engineered into the genome of aparticular soybean plant may then be moved into the genome of anothervariety using traditional breeding techniques that are well known in theplant breeding arts. For example, a backcrossing approach is commonlyused to move a transgene from a transformed soybean variety into analready developed soybean variety, and the resulting backcrossconversion plant would then comprise the transgene(s).

Various genetic elements can be introduced into the plant genome usingtransformation. These elements include, but are not limited to genes,coding sequences, inducible, constitutive, and tissue specificpromoters, enhancing sequences, and signal and targeting sequences. Forexample, see the traits, genes and transformation methods listed in U.S.Pat. No. 6,118,055.

Plant transformation involves the construction of an expression vectorwhich will function in plant cells. Such a vector comprises DNAcomprising a gene under control of, or operatively linked to, aregulatory element (for example, a promoter). The expression vector maycontain one or more such operably linked gene/regulatory elementcombinations. The vector(s) may be in the form of a plasmid and can beused alone or in combination with other plasmids to provide transformedsoybean plants using transformation methods as described below toincorporate transgenes into the genetic material of the soybeanplant(s).

Expression Vectors for Soybean Transformation: Marker Genes

Expression vectors include at least one genetic marker operably linkedto a regulatory element (a promoter, for example) that allowstransformed cells containing the marker to be either recovered bynegative selection, i.e., inhibiting growth of cells that do not containthe selectable marker gene, or by positive selection, i.e., screeningfor the product encoded by the genetic marker. Many commonly usedselectable marker genes for plant transformation are well known in thetransformation arts, and include, for example, genes that code forenzymes that metabolically detoxify a selective chemical agent which maybe an antibiotic or an herbicide, or genes that encode an altered targetwhich is insensitive to the inhibitor. A few positive selection methodsare also known in the art.

One commonly used selectable marker gene for plant transformation is theneomycin phosphotransferase II (nptII) gene which, when under thecontrol of plant regulatory signals, confers resistance to kanamycin.Fraley et al., Proc. Natl. Acad. Sci. USA, 80:4803 (1983). Anothercommonly used selectable marker gene is the hygromycinphosphotransferase gene which confers resistance to the antibiotichygromycin. Vanden Elzen et al., Plant Mol. Biol., 5:299 (1985).

Additional selectable marker genes of bacterial origin that conferresistance to antibiotics include gentamycin acetyl transferase,streptomycin phosphotransferase and aminoglycoside-3′-adenyltransferase, the bleomycin resistance determinant (Hayford et al., PlantPhysiol. 86:1216 (1988), Jones et al., Mol. Gen. Genet., 210:86 (1987),Svab et al., Plant Mol. Biol. 14:197 (1990), Hille et al., Plant Mol.Biol. 7:171 (1986)). Other selectable marker genes confer resistance toherbicides such as glyphosate, glufosinate or bromoxynil (Comai et al.,Nature 317:741-744 (1985), Gordon-Kamm et al., Plant Cell 2:603-618(1990) and Stalker et al., Science 242:419-423 (1988)).

Selectable marker genes for plant transformation not of bacterial origininclude, for example, mouse dihydrofolate reductase, plant5-enolpyruvylshikimate-3-phosphate synthase and plant acetolactatesynthase (Eichholtz et al., Somatic Cell Mol. Genet. 13:67 (1987), Shahet al., Science 233:478 (1986), Charest et al., Plant Cell Rep. 8:643(1990)).

Another class of marker genes for plant transformation requiresscreening of presumptively transformed plant cells rather than directgenetic selection of transformed cells for resistance to a toxicsubstance such as an antibiotic. These genes are particularly useful toquantify or visualize the spatial pattern of expression of a gene inspecific tissues and are frequently referred to as reporter genesbecause they can be fused to a gene or gene regulatory sequence for theinvestigation of gene expression. Commonly used genes for screeningpresumptively transformed cells include β-glucuronidase (GUS),β-galactosidase, luciferase and chloramphenicol acetyltransferase(Jefferson, R. A., Plant Mol. Biol. Rep. 5:387 (1987), Teeri et al.,EMBO J. 8:343 (1989), Koncz et al., Proc. Natl. Acad. Sci. USA 84:131(1987), DeBlock et al., EMBO J. 3:1681 (1984)).

In vivo methods for visualizing GUS activity that do not requiredestruction of plant tissue are available (Molecular Probes publication2908, IMAGENE GREEN, p. 1-4 (1993) and Naleway et al., J. Cell Biol.115:151 a (1991)). However, these in vivo methods for visualizing GUSactivity have not proven useful for recovery of transformed cellsbecause of low sensitivity, high fluorescent backgrounds and limitationsassociated with the use of luciferase genes as selectable markers.

More recently, a gene encoding Green Fluorescent Protein (GFP) has beenutilized as a marker for gene expression in prokaryotic and eukaryoticcells (Chalfie et al., Science 263:802 (1994)). GFP and mutants of GFPmay be used as screenable markers.

Expression Vectors for Soybean Transformation: Promoters

Genes included in expression vectors must be driven by a nucleotidesequence comprising a regulatory element, for example, a promoter.Several types of promoters are well known in the transformation arts asare other regulatory elements that can be used alone or in combinationwith promoters.

As used herein, “promoter” includes reference to a region of DNAupstream from the start of transcription and involved in recognition andbinding of RNA polymerase and other proteins to initiate transcription.A “plant promoter” is a promoter capable of initiating transcription inplant cells. Examples of promoters under developmental control includepromoters that preferentially initiate transcription in certain tissues,such as leaves, roots, seeds, fibers, xylem vessels, tracheids, orsclerenchyma. Such promoters are referred to as “tissue-preferred”.Promoters that initiate transcription only in a certain tissue arereferred to as “tissue-specific”. A “cell-type” specific promoterprimarily drives expression in certain cell types in one or more organs,for example, vascular cells in roots or leaves. An “inducible” promoteris a promoter which is under environmental control. Examples ofenvironmental conditions that may effect transcription by induciblepromoters include anaerobic conditions or the presence of light.Tissue-specific, tissue-preferred, cell type specific, and induciblepromoters constitute the class of “non-constitutive” promoters. A“constitutive” promoter is a promoter that is active under mostenvironmental conditions.

A. Inducible Promoters—An inducible promoter is operably linked to agene for expression in soybean. Optionally, the inducible promoter isoperably linked to a nucleotide sequence encoding a signal sequencewhich is operably linked to a gene for expression in soybean. With aninducible promoter the rate of transcription increases in response to aninducing agent.

Any inducible promoter can be used in the instant invention. See Ward etal., Plant Mol. Biol. 22:361-366 (1993). Exemplary inducible promotersinclude, but are not limited to, that from the ACEI system whichresponds to copper (Mett et al., Proc. Natl. Acad. Sci. USA 90:4567-4571(1993)); In2 gene from maize which responds to benzenesulfonamideherbicide safeners (Hershey et al., Mol. Gen. Genetics 227:229-237(1991) and Gatz et al., Mol. Gen. Genetics 243:32-38 (1994)) or Tetrepressor from Tn10 (Gatz et al., Mol. Gen. Genetics 227:229-237(1991)). A particularly preferred inducible promoter is a promoter thatresponds to an inducing agent to which plants do not normally respond.An exemplary inducible promoter is the inducible promoter from a steroidhormone gene, the transcriptional activity of which is induced by aglucocorticosteroid hormone (Schena et al., Proc. Natl. Acad. Sci. USA88:0421 (1991)).

B. Constitutive Promoters—A constitutive promoter is operably linked toa gene for expression in soybean or the constitutive promoter isoperably linked to a nucleotide sequence encoding a signal sequencewhich is operably linked to a gene for expression in soybean.

Many different constitutive promoters can be utilized in the instantinvention. Exemplary constitutive promoters include, but are not limitedto, the promoters from plant viruses such as the 35S promoter from CaMV(Odell et al., Nature 313:810-812 (1985)) and the promoters from suchgenes as rice actin (McElroy et al., Plant Cell 2: 163-171 (1990));ubiquitin (Christensen et al., Plant Mol. Biol. 12:619-632 (1989) andChristensen et al., Plant Mol. Biol. 18:675-689 (1992)); PEMU (Last etal., Theor. Appl. Genet. 81:581-588 (1991)); MAS (Velten et al., EMBO J.3:2723-2730 (1984)) and maize H3 histone (Lepetit et al., Mol. Gen.Genetics 231:276-285 (1992) and Atanassova et al., Plant Journal 2 (3):291-300 (1992)). The ALS promoter, Xba1/NcoI fragment 5′ to the Brassicanapus ALS3 structural gene (or a nucleotide sequence similarity to saidXba1/NcoI fragment), represents a particularly useful constitutivepromoter. See PCT application WO 96/30530.

C. Tissue-specific or Tissue-preferred Promoters—A tissue-specificpromoter is operably linked to a gene for expression in soybean.Optionally, the tissue-specific promoter is operably linked to anucleotide sequence encoding a signal sequence which is operably linkedto a gene for expression in soybean. Plants transformed with a gene ofinterest operably linked to a tissue-specific promoter produce theprotein product of the transgene exclusively, or preferentially, in aspecific tissue.

Any tissue-specific or tissue-preferred promoter can be utilized in theinstant invention. Exemplary tissue-specific or tissue-preferredpromoters include, but are not limited to, a root-preferred promotersuch as that from the phaseolin gene (Murai et al., Science 23:476-482(1983) and Sengupta-Gopalan et al., Proc. Natl. Acad. Sci. USA82:3320-3324 (1985)); a leaf-specific and light-induced promoter such asthat from cab or rubisco (Simpson et al., EMBO J. 4(11):2723-2729 (1985)and Timko et al., Nature 318:579-582 (1985)); an anther-specificpromoter such as that from LAT52 (Twell et al., Mol. Gen. Genetics217:240-245 (1989)); a pollen-specific promoter such as that from Zm13(Guerrero et al., Mol. Gen. Genetics 244:161-168 (1993)) or amicrospore-preferred promoter such as that from apg (Twell et al., Sex.Plant Reprod. 6:217-224 (1993)).

Signal Sequences for Targeting Proteins to Subcellular Compartments

Transport of a protein produced by transgenes to a subcellularcompartment such as the chloroplast, vacuole, peroxisome, glyoxysome,cell wall or mitochondrion or for secretion into the apoplast, isaccomplished by means of operably linking the nucleotide sequenceencoding a signal sequence to the 5′ and/or 3′ region of a gene encodingthe protein of interest. Targeting sequences at the 5′ and/or 3′ end ofthe structural gene may determine during protein synthesis andprocessing where the encoded protein is ultimately compartmentalized.

The presence of a signal sequence directs a polypeptide to either anintracellular organelle or subcellular compartment or for secretion tothe apoplast. Many signal sequences are known in the art. See, forexample, Becker et al., Plant Mol. Biol. 20:49 (1992); Knox, C., et al.,Plant Mol. Biol. 9:3-17 (1987); Lerner et al., Plant Physiol. 91:124-129(1989); Frontes et al., Plant Cell 3:483-496 (1991); Matsuoka et al.,Proc. Natl. Acad. Sci. 88:834 (1991); Gould et al., J. Cell. Biol.108:1657 (1989); Creissen et al., Plant J. 2:129 (1991); Kalderon, etal., Cell 39:499-509 (1984); Steifel, et al., Plant Cell 2:785-793(1990).

Foreign Protein Genes and Agronomic Genes

With transgenic plants according to the present invention, a foreignprotein can be produced in commercial quantities. Thus, techniques forthe selection and propagation of transformed plants, which are wellunderstood in the art, yield a plurality of transgenic plants which areharvested in a conventional manner, and a foreign protein then can beextracted from a tissue of interest or from total biomass. Proteinextraction from plant biomass can be accomplished by known methods whichare discussed, for example, by Heney and Orr, Anal. Biochem. 114:92-6(1981).

According to a preferred embodiment, the transgenic plant provided forcommercial production of foreign protein is a soybean plant. In anotherpreferred embodiment, the biomass of interest is seed. For therelatively small number of transgenic plants that show higher levels ofexpression, a genetic map can be generated, primarily via conventionalRFLP, PCR and SSR analysis, which identifies the approximate chromosomallocation of the integrated DNA molecule. For exemplary methodologies inthis regard, see Glick and Thompson, Methods in Plant Molecular Biologyand Biotechnology, CRC Press, Boca Raton 269:284 (1993). Map informationconcerning chromosomal location is useful for proprietary protection ofa subject transgenic plant.

Wang et al. discuss “Large Scale Identification, Mapping and Genotypingof Single-Nucleotide Polymorphisms in the Human Genome”, Science,280:1077-1082, 1998, and similar capabilities are becoming increasinglyavailable for the soybean genome. Map information concerning chromosomallocation is useful for proprietary protection of a subject transgenicplant. If unauthorized propagation is undertaken and crosses made withother germplasm, the map of the integration region can be compared tosimilar maps for suspect plants to determine if the latter have a commonparentage with the subject plant. Map comparisons would involvehybridizations, RFLP, PCR, SSR and sequencing, all of which areconventional techniques. SNPs may also be used alone or in combinationwith other techniques.

Likewise, by means of the present invention, plants can be geneticallyengineered to express various phenotypes of agronomic interest. Throughthe transformation of soybean the expression of genes can be altered toenhance disease resistance, insect resistance, herbicide resistance,agronomic, grain quality and other traits. Transformation can also beused to insert DNA sequences which control or help controlmale-sterility. DNA sequences native to soybean as well as non-nativeDNA sequences can be transformed into soybean and used to alter levelsof native or non-native proteins. Various promoters, targetingsequences, enhancing sequences, and other DNA sequences can be insertedinto the genome for the purpose of altering the expression of proteins.Reduction of the activity of specific genes (also known as genesilencing, or gene suppression) is desirable for several aspects ofgenetic engineering in plants.

Many techniques for gene silencing are well known to one of skill in theart, including but not limited to knock-outs (such as by insertion of atransposable element such as mu (Vicki Chandler, The Maize Handbook ch.118 (Springer-Verlag 1994) or other genetic elements such as a FRT, Loxor other site specific integration site, antisense technology (see,e.g., Sheehy et al. (1988) PNAS USA 85:8805-8809; and U.S. Pat. Nos.5,107,065; 5,453,566; and 5,759,829); co-suppression (e.g., Taylor(1997) Plant Cell 9:1245; Jorgensen (1990) Trends Biotech.8(12):340-344; Flavell (1994) PNAS USA 91:3490-3496; Finnegan et al.(1994) Bio/Technology 12: 883-888; and Neuhuber et al. (1994) Mol. Gen.Genet. 244:230-241); RNA interference (Napoli et al. (1990) Plant Cell2:279-289; U.S. Pat. No. 5,034,323; Sharp (1999) Genes Dev. 13:139-141;Zamore et al. (2000) Cell 101:25-33; and Montgomery et al. (1998) PNASUSA 95:15502-15507), virus-induced gene silencing (Burton, et al. (2000)Plant Cell 12:691-705; and Baulcombe (1999) Curr. Op. Plant Bio.2:109-113); target-RNA-specific ribozymes (Haseloff et al. (1988) Nature334: 585-591); hairpin structures (Smith et al. (2000) Nature407:319-320; WO 99/53050; and WO 98/53083); MicroRNA (Aukerman & Sakai(2003) Plant Cell 15:2730-2741); ribozymes (Steinecke et al. (1992) EMBOJ. 11:1525; and Perriman et al. (1993) Antisense Res. Dev. 3:253);oligonucleotide mediated targeted modification (e.g., WO 03/076574 andWO 99/25853); Zn-finger targeted molecules (e.g., WO 01/52620; WO03/048345; and WO 00/42219); and other methods or combinations of theabove methods known to those of skill in the art.

Likewise, by means of the present invention, agronomic genes can beexpressed in transformed plants. More particularly, plants can begenetically engineered to express various phenotypes of agronomicinterest. Exemplary genes implicated in this regard include, but are notlimited to, those categorized below:

1. Genes That Confer Resistance to Pests or Disease and That Encode:

A. Plant disease resistance genes. Plant defenses are often activated byspecific interaction between the product of a disease resistance gene(R) in the plant and the product of a corresponding avirulence (Avr)gene in the pathogen. A plant variety can be transformed with one ormore cloned resistance genes to engineer plants that are resistant tospecific pathogen strains. See, for example Jones et al., Science266:789 (1994) (cloning of the tomato Cf-9 gene for resistance toCladosporium fulvum); Martin et al., Science 262:1432 (1993) (tomato Ptogene for resistance to Pseudomonas syringae pv. tomato encodes a proteinkinase); Mindrinos et al. Cell 78:1089 (1994) (Arabidopsis RSP2 gene forresistance to Pseudomonas syringae), McDowell & Woffenden, (2003) TrendsBiotechnol. 21(4): 178-83 and Toyoda et al., (2002) Transgenic Res. 11(6):567-82.

B. A gene conferring resistance to a pest, such as soybean cystnematode. See e.g., PCT Application WO 96/30517; PCT Application WO93/19181.

C. A Bacillus thuringiensis protein, a derivative thereof or a syntheticpolypeptide modeled thereon. See, for example, Geiser et al., Gene48:109 (1986), who disclose the cloning and nucleotide sequence of a Btδ-endotoxin gene. Moreover, DNA molecules encoding δ-endotoxin genes canbe purchased from American Type Culture Collection, Manassas, Va., forexample, under ATCC Accession Nos. 40098, 67136, 31995 and 31998.

D. A lectin. See, for example, Van Damme et al., Plant Molec. Biol.24:25 (1994), who disclose the nucleotide sequences of several Cliviaminiata mannose-binding lectin genes.

E. A vitamin-binding protein such as avidin. See PCT application US93/06487 which teaches the use of avidin and avidin homologues aslarvicides against insect pests.

F. An enzyme inhibitor, for example, a protease or proteinase inhibitoror an amylase inhibitor. See, for example, Abe et al., J. Biol. Chem.262:16793 (1987) (nucleotide sequence of rice cysteine proteinaseinhibitor), Huub et al., Plant Molec. Biol. 21:985 (1993) (nucleotidesequence of cDNA encoding tobacco proteinase inhibitor I), Sumitani etal., Biosci. Biotech. Biochem. 57:1243 (1993) (nucleotide sequence ofStreptomyces nitrosporeus α-amylase inhibitor) and U.S. Pat. No.5,494,813 (Hepher and Atkinson, issued Feb. 27, 1996).

G. An insect-specific hormone or pheromone such as an ecdysteroid orjuvenile hormone, a variant thereof, a mimetic based thereon, or anantagonist or agonist thereof. See, for example, the disclosure byHammock et al., Nature 344:458 (1990), of baculovirus expression ofcloned juvenile hormone esterase, an inactivator of juvenile hormone.

H. An insect-specific peptide or neuropeptide which, upon expression,disrupts the physiology of the affected pest. For example, see thedisclosures of Regan, J. Biol. Chem. 269:9 (1994) (expression cloningyields DNA coding for insect diuretic hormone receptor), and Pratt etal., Biochem. Biophys. Res. Comm. 163:1243 (1989) (an allostatin isidentified in Diploptera puntata); Chattopadhyay et al. (2004) CriticalReviews in Microbiology 30 (1): 33-54 2004; Zjawiony (2004) J Nat Prod67 (2): 300-310; Carlini & Grossi-de-Sa (2002) Toxicon, 40 (11):1515-1539; Ussuf et al. (2001) Curr Sci. 80 (7): 847-853; andVasconcelos & Oliveira (2004) Toxicon 44 (4): 385-403. See also U.S.Pat. No. 5,266,317 to Tomalski et al., which discloses genes encodinginsect-specific, paralytic neurotoxins.

I. An insect-specific venom produced in nature by a snake, a wasp, etc.For example, see Pang et al., Gene 116:165 (1992), for disclosure ofheterologous expression in plants of a gene coding for a scorpioninsectotoxic peptide.

J. An enzyme responsible for a hyperaccumulation of a monoterpene, asesquiterpene, a steroid, hydroxamic acid, a phenylpropanoid derivativeor another non-protein molecule with insecticidal activity.

K. An enzyme involved in the modification, including thepost-translational modification, of a biologically active molecule; forexample, a glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme,a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, aphosphatase, a kinase, a phosphorylase, a polymerase, an elastase, achitinase and a glucanase, whether natural or synthetic. See PCTapplication WO 93/02197 (Scott et al.), which discloses the nucleotidesequence of a callase gene. DNA molecules which containchitinase-encoding sequences can be obtained, for example, from the ATCCunder Accession Nos. 39637 and 67152. See also Kramer et al., InsectBiochem. Molec. Biol. 23:691 (1993), who teach the nucleotide sequenceof a cDNA encoding tobacco hornworm chitinase, and Kawalleck et al.,Plant Molec. Biol. 21:673 (1993), who provide the nucleotide sequence ofthe parsley ubi4-2 polyubiquitin gene, U.S. Pat. Nos. 7,145,060,7,087,810 and 6,563,020.

L. A molecule that stimulates signal transduction. For example, see thedisclosure by Botella et al., Plant Molec. Biol. 24:757 (1994), ofnucleotide sequences for mung bean calmodulin cDNA clones, and Griess etal., Plant Physiol. 104:1467 (1994), who provide the nucleotide sequenceof a maize calmodulin cDNA clone.

M. A hydrophobic moment peptide. See PCT application WO 95/16776 andU.S. Pat. No. 5,580,852, which disclose peptide derivatives oftachyplesin which inhibit fungal plant pathogens, and PCT application WO95/18855 and U.S. Pat. No. 5,607,914 which teaches syntheticantimicrobial peptides that confer disease resistance.

N. A membrane permease, a channel former or a channel blocker. Forexample, see the disclosure of Jaynes et al., Plant Sci 89:43 (1993), ofheterologous expression of a cecropin-β lytic peptide analog to rendertransgenic tobacco plants resistant to Pseudomonas solanacearum.

O. A viral-invasive protein or a complex toxin derived therefrom. Forexample, the accumulation of viral coat proteins in transformed plantcells imparts resistance to viral infection and/or disease developmenteffected by the virus from which the coat protein gene is derived, aswell as by related viruses. See Beachy et al., Ann. Rev. Phytopathol.28:451 (1990). Coat protein-mediated resistance has been conferred upontransformed plants against alfalfa mosaic virus, cucumber mosaic virusand tobacco mosaic virus.

P. An insect-specific antibody or an immunotoxin derived therefrom.Thus, an antibody targeted to a critical metabolic function in theinsect gut would inactivate an affected enzyme, killing the insect. SeeTaylor et al., Abstract #497, Seventh Int'l Symposium on MolecularPlant-Microbe Interactions (Edinburgh, Scotland) (1994) (enzymaticinactivation in transgenic tobacco via production of single-chainantibody fragments).

Q. A virus-specific antibody. See, for example, Tavladoraki et al.,Nature 366:469 (1993), who show that transgenic plants expressingrecombinant antibody genes are protected from virus attack.

R. A developmental-arrestive protein produced in nature by a pathogen ora parasite. Thus, fungal endo-α-1,4-D-polygalacturonases facilitatefungal colonization and plant nutrient release by solubilizing plantcell wall homo-α-1,4-D-galacturonase. See Lamb et al., Bio/Technology10:1436 (1992). The cloning and characterization of a gene which encodesa bean endopolygalacturonase-inhibiting protein is described by Toubartet al., Plant J. 2:367 (1992).

S. A developmental-arrestive protein produced in nature by a plant. Forexample, Logemann et al., Bio/Technology 10:305 (1992), have shown thattransgenic plants expressing the barley ribosome-inactivating gene havean increased resistance to fungal disease.

T. Genes involved in the Systemic Acquired Resistance (SAR) Responseand/or the pathogenesis-related genes. Briggs, S., Current Biology, 5(2)(1995); Pieterse & Van Loon (2004) Curr. Opin. Plant Bio. 7(4):456-64and Somssich (2003) Cell 113(7):815-6.

U. Antifungal genes. See Cornelissen and Melchers, Plant Physiol.,101:709-712 (1993); Parijs et al., Planta 183:258-264 (1991) andBushnell et al., Can. J. of Plant Path. 20(2):137-149 (1998). Also seeU.S. Pat. No. 6,875,907.

V. Detoxification genes, such as for fumonisin, beauvericin,moniliformin and zearalenone and their structurally related derivatives.For example, see U.S. Pat. No. 5,792,931.

W. Cystatin and cysteine proteinase inhibitors. See U.S. Pat. No.7,205,453.

X. Defensin genes. See WO 03/000863 and U.S. Pat. No. 6,911,577.

Y. Genes conferring resistance to nematodes, and in particular soybeancyst nematodes. See e.g. PCT Application WO 96/30517; PCT Application WO93/19181, WO 03/033651 and Urwin et al., Planta 204:472-479 (1998),Williamson (1999) Curr Opin Plant Bio. 2(4):327-31.

Z. Genes that confer resistance to Phytophthora root rot, such as theRps 1, Rps 1-a, Rps 1-b, Rps 1-c, Rps 1-d, Rps 1-e, Rps 1-k, Rps 2, Rps3-a, Rps 3-b, Rps 3-c, Rps 4, Rps 5, Rps 6, Rps 7 and other Rps genes.See, for example, Shoemaker et al., Phytophthora Root Rot ResistanceGene Mapping in Soybean, Plant Genome IV Conference, San Diego, Calif.(1995).

AA. Genes that confer resistance to Brown Stem Rot, such as described inU.S. Pat. No. 5,689,035 and incorporated by reference for this purpose.

2. Genes that Confer Resistance to an Herbicide, for Example:

A. An herbicide that inhibits the growing point or meristem, such as animidazolinone or a sulfonylurea. Exemplary genes in this category codefor mutant ALS and AHAS enzyme as described, for example, by Lee et al.,EMBO J. 7:1241 (1988), and Miki et al., Theor. Appl. Genet. 80:449(1990), respectively.

B. Glyphosate (resistance conferred by mutant5-enolpyruvlshikimate-3-phosphate synthase (EPSPS) and aroA genes,respectively) and other phosphono compounds such as glufosinate(phosphinothricin acetyl transferase (PAT) and Streptomyceshygroscopicus PAT bar genes), and pyridinoxy or phenoxy proprionic acidsand cyclohexanediones (ACCase inhibitor-encoding genes). See, forexample, U.S. Pat. No. 4,940,835 to Shah, et al., which discloses thenucleotide sequence of a form of EPSPS which can confer glyphosateresistance. U.S. Pat. No. 5,627,061 to Barry et al. also describes genesencoding EPSPS enzymes. See also U.S. Pat. Nos. 6,566,587; 6,338,961;6,248,876 B1; 6,040,497; 5,804,425; 5,633,435; 5,145,783; 4,971,908;5,312,910; 5,188,642; 4,940,835; 5,866,775; 6,225,114 B1; 6,130,366;5,310,667; 4,535,060; 4,769,061; 5,633,448; 5,510,471; Re. 36,449; RE37,287 E; and 5,491,288; and international publications EP1173580; WO01/66704; EP1173581 and EP1173582, which are incorporated herein byreference for this purpose. Glyphosate resistance is also imparted toplants that express a gene that encodes a glyphosate oxido-reductaseenzyme as described more fully in U.S. Pat. Nos. 5,776,760 and5,463,175, which are incorporated herein by reference for this purpose.In addition glyphosate resistance can be imparted to plants by the overexpression of genes encoding glyphosate N-acetyltransferase. See, forexample, U.S. application Ser. No. 10/427,692. A DNA molecule encoding amutant aroA gene can be obtained under ATCC accession number 39256, andthe nucleotide sequence of the mutant gene is disclosed in U.S. Pat. No.4,769,061 to Comai. European patent application No. 0 333 033 to Kumadaet al., and U.S. Pat. No. 4,975,374 to Goodman et al., disclosenucleotide sequences of glutamine synthetase genes which conferresistance to herbicides such as L-phosphinothricin. The nucleotidesequence of a PAT gene is provided in European application No. 0 242 246to Leemans et al. DeGreef et al., Bio/Technology 7:61 (1989) describethe production of transgenic plants that express chimeric bar genescoding for phosphinothricin acetyl transferase activity. Exemplary ofgenes conferring resistance to phenoxy proprionic acids andcyclohexones, such as sethoxydim and haloxyfop are the Acc1-S1, Acc1-S2,and Acc2-S3 genes described by Marshall et al., Theor. Appl. Genet.83:435 (1992).

C. An herbicide that inhibits photosynthesis, such as a triazine (psbAand gs+genes) and a benzonitrile (nitrilase gene). Przibila et al.,Plant Cell 3:169 (1991), describe the transformation of Chlamydomonaswith plasmids encoding mutant psbA genes. Nucleotide sequences fornitrilase genes are disclosed in U.S. Pat. No. 4,810,648 to Stalker andDNA molecules containing these genes are available under ATCC AccessionNos. 53435, 67441 and 67442. Cloning and expression of DNA coding for aglutathione S-transferase is described by Hayes et al., Biochem. J.285:173 (1992).

D. Acetohydroxy acid synthase, which has been found to make plants thatexpress this enzyme resistant to multiple types of herbicides, has beenintroduced into a variety of plants. See Hattori et al., Mol. Gen.Genet. 246:419, 1995. Other genes that confer tolerance to herbicidesinclude a gene encoding a chimeric protein of rat cytochrome P4507A1 andyeast NADPH-cytochrome P450 oxidoreductase (Shiota et al., PlantPhysiol., 106:17, 1994), genes for glutathione reductase and superoxidedismutase (Aono et al., Plant Cell Physiol. 36:1687, 1995), and genesfor various phosphotransferases (Datta et al., Plant Mol. Biol. 20:619,1992).

E. Protoporphyrinogen oxidase (protox) is necessary for the productionof chlorophyll, which is necessary for all plant survival. The protoxenzyme serves as the target for a variety of herbicidal compounds. Theseherbicides also inhibit growth of all the different species of plantspresent, causing their total destruction. The development of plantscontaining altered protox activity which are resistant to theseherbicides are described in U.S. Pat. Nos. 6,288,306; 6,282,837;5,767,373; and international publication WO 01/12825.

3. Genes that Confer or Contribute to a Value-Added Trait, such as:

A. Modified fatty acid metabolism, for example, by transforming a plantwith an antisense gene of stearyl-ACP desaturase to increase stearicacid content of the plant. See Knultzon et al., Proc. Natl. Acad. Sci.USA 89:2625 (1992).

B. Decreased phytate content—1) Introduction of a phytase-encoding geneenhances breakdown of phytate, adding more free phosphate to thetransformed plant. For example, see Van Hartingsveldt et al., Gene127:87 (1993), for a disclosure of the nucleotide sequence of anAspergillus niger phytase gene. 2) Up-regulation of a gene that reducesphytate content. In maize, this, for example, could be accomplished, bycloning and then re-introducing DNA associated with one or more of thealleles, such as the LPA alleles, identified in maize mutantscharacterized by low levels of phytic acid, such as in Raboy et al.,Maydica 35: 383 (1990) and/or by altering inositol kinase activity as inWO 02/059324, US2003/000901 1, WO 03/027243, US2003/0079247, WO99/05298, U.S. Pat. No. 6,197,561, U.S. Pat. No. 6,291,224, U.S. Pat.No. 6,391,348, WO 2002/059324, U.S. Pat. No. 2003/0079247, WO98/45448,WO99/55882, WO01/04147.

C. Modified carbohydrate composition effected, for example, bytransforming plants with a gene coding for an enzyme that alters thebranching pattern of starch, or, a gene altering thioredoxin such as NTRand/or TRX (See U.S. Pat. No. 6,531,648 which is incorporated byreference for this purpose) and/or a gamma zein knock out or mutant suchas cs27 or TUSC27 or en27 (See U.S. Pat. No. 6,858,778 andUS2005/0160488, US2005/0204418; which are incorporated by reference forthis purpose). See Shiroza et al., J. Bacteriol. 170: 810 (1988)(nucleotide sequence of Streptococcus mutans fructosyltransferase gene),Steinmetz et al., Mol. Gen. Genet. 200: 220 (1985) (nucleotide sequenceof Bacillus subtilis levansucrase gene), Pen et al., Bio/Technology 10:292 (1992) (production of transgenic plants that express Bacilluslicheniformis alpha-amylase), Elliot et al., Plant Molec. Biol. 21: 515(1993) (nucleotide sequences of tomato invertase genes), Sogaard et al.,J. Biol. Chem. 268: 22480 (1993) (site-directed mutagenesis of barleyalpha-amylase gene), and Fisher et al., Plant Physiol. 102: 1045 (1993)(maize endosperm starch branching enzyme II), WO 99/10498 (improveddigestibility and/or starch extraction through modification ofUDP-D-xylose 4-epimerase, Fragile 1 and 2, Ref 1, HCHL, C4H), U.S. Pat.No. 6,232,529 (method of producing high oil seed by modification ofstarch levels (AGP)). The fatty acid modification genes mentioned abovemay also be used to affect starch content and/or composition through theinterrelationship of the starch and oil pathways.

D. Elevated oleic acid via FAD-2 gene modification and/or decreasedlinolenic acid via FAD-3 gene modification. See U.S. Pat. Nos.6,063,947; 6,323,392; and international publication WO 93/11245.Linolenic acid is one of the five most abundant fatty acids in soybeanseeds. The low oxidative stability of linolenic acid is one reason thatsoybean oil undergoes partial hydrogenation. When partiallyhydrogenated, all unsaturated fatty acids form trans fats. Soybeans arethe largest source of edible-oils in the U.S. and 40% of soybean oilproduction is partially hydrogenated. The consumption of trans fatsincreases the risk of heart disease. Regulations banning trans fats haveencouraged the development of low linolenic soybeans. Soybeanscontaining low linolenic acid percentages create a more stable oilrequiring hydrogenation less often. This provides trans fat freealternatives in products such as cooking oil.

E. Altering conjugated linolenic or linoleic acid content, such as in WO01/12800. Altering LEC1, AGP, Dek1, Superal1,mi1ps, various Ipa genessuch as Ipa1, Ipa3, hpt or hggt. For example, see WO 02/42424, WO98/22604, WO 03/011015, U.S. Pat. No. 6,423,886, U.S. Pat. Nos.6,197,561, 6,825,397, 7,157,621 and US 2003/0079247, WO 02/057439, WO03/011015 and Rivera-Madrid, R. et al. Proc. Natl. Acad. Sci.92:5620-5624 (1995).

F. Altered antioxidant content or composition, such as alteration oftocopherol or tocotrienols. For example, see U.S. Pat. Nos. 6,787,683and 7,154,029 and WO 00/68393 involving the manipulation of antioxidantlevels through alteration of a phytl prenyl transferase (ppt), WO03/082899 through alteration of a homogentisate geranyl geranyltransferase (hggt).

G. Altered essential seed amino acids. For example, see U.S. Pat. No.6,127,600 (method of increasing accumulation of essential amino acids inseeds), U.S. Pat. No. 6,080,913 (binary methods of increasingaccumulation of essential amino acids in seeds), U.S. Pat. No. 5,990,389(high lysine), WO 99/40209 (alteration of amino acid compositions inseeds), WO 99/29882 (methods for altering amino acid content ofproteins), U.S. Pat. No. 5,850,016 (alteration of amino acidcompositions in seeds), WO 98/20133 (proteins with enhanced levels ofessential amino acids), U.S. Pat. No. 5,885,802 (high methionine), U.S.Pat. No. 5,885,801 (high threonine), U.S. Pat. No. 6,664,445 (plantamino acid biosynthetic enzymes), U.S. Pat. No. 6,459,019 (increasedlysine and threonine), U.S. Pat. No. 6,441,274 (plant tryptophansynthase beta subunit), U.S. Pat. No. 6,346,403 (methionine metabolicenzymes), U.S. Pat. No. 5,939,599 (high sulfur), U.S. Pat. No. 5,912,414(increased methionine), WO 98/56935 (plant amino acid biosyntheticenzymes), WO 98/45458 (engineered seed protein having higher percentageof essential amino acids), WO 98/42831 (increased lysine), U.S. Pat. No.5,633,436 (increasing sulfur amino acid content), U.S. Pat. No.5,559,223 (synthetic storage proteins with defined structure containingprogrammable levels of essential amino acids for improvement of thenutritional value of plants), WO 96/01905 (increased threonine), WO95/15392 (increased lysine), U.S. Pat. Nos. 6,930,225, 7,179,955, U.S.Publication No. 2004/0068767, U.S. Pat. No. 6,803,498, WO 01/79516, andWO 00/09706 (Ces A: cellulose synthase), U.S. Pat. No. 6,194,638(hemicellulose), U.S. Pat. No. 6,399,859 and U.S. Pat. No. 7,098,381(UDPGdH), U.S. Pat. No. 6,194,638 (RGP).

4. Genes that Control Male Sterility

There are several methods of conferring genetic male sterilityavailable, such as multiple mutant genes at separate locations withinthe genome that confer male sterility, as disclosed in U.S. Pat. Nos.4,654,465 and 4,727,219 to Brar et al. and chromosomal translocations asdescribed by Patterson in U.S. Pat. Nos. 3,861,709 and 3,710,511. Inaddition to these methods, Albertsen et al., U.S. Pat. No. 5,432,068,describe a system of nuclear male sterility which includes: identifyinga gene which is critical to male fertility; silencing this native genewhich is critical to male fertility; removing the native promoter fromthe essential male fertility gene and replacing it with an induciblepromoter; inserting this genetically engineered gene back into theplant; and thus creating a plant that is male sterile because theinducible promoter is not “on” resulting in the male fertility gene notbeing transcribed. Fertility is restored by inducing, or turning “on”,the promoter, which in turn allows the gene that confers male fertilityto be transcribed.

A. Introduction of a deacetylase gene under the control of atapetum-specific promoter and with the application of the chemicalN-Ac-PPT. See international publication WO 01/29237.

B. Introduction of various stamen-specific promoters. See internationalpublications WO 92/13956 and WO 92/13957.

C. Introduction of the barnase and the barstar genes. See Paul et al.,Plant Mol. Biol. 19:611-622, 1992).

For additional examples of nuclear male and female sterility systems andgenes, see also, U.S. Pat. No. 5,859,341; U.S. Pat. No. 6,297,426; U.S.Pat. No. 5,478,369; U.S. Pat. No. 5,824,524; U.S. Pat. No. 5,850,014;and U.S. Pat. No. 6,265,640; all of which are hereby incorporated byreference.

5. Genes that Create a Site for Site Specific DNA Integration.

This includes the introduction of FRT sites that may be used in theFLP/FRT system and/or Lox sites that may be used in the Cre/Loxp system.For example, see Lyznik, et al., Site-Specific Recombination for GeneticEngineering in Plants, Plant Cell Rep (2003) 21:925-932 and WO 99/25821,which are hereby incorporated by reference. Other systems that may beused include the Gln recombinase of phage Mu (Maeser et al., 1991; VickiChandler, The Maize Handbook ch. 118 (Springer-Verlag 1994), the Pinrecombinase of E. coli (Enomoto et al., 1983), and the R/RS system ofthe pSR1 plasmid (Araki et al., 1992).

6. Genes that Affect Abiotic Stress Resistance.

Genes that affect abiotic stress resistance (including but not limitedto flowering, pod and seed development, enhancement of nitrogenutilization efficiency, altered nitrogen responsiveness, droughtresistance or tolerance, cold resistance or tolerance, and saltresistance or tolerance) and increased yield under stress. For example,see: WO 00/73475 where water use efficiency is altered throughalteration of malate; U.S. Pat. No. 5,892,009, U.S. Pat. No. 5,965,705,U.S. Pat. No. 5,929,305, U.S. Pat. No. 5,891,859, U.S. Pat. No.6,417,428, U.S. Pat. No. 6,664,446, U.S. Pat. No. 6,706,866, U.S. Pat.No. 6,717,034, U.S. Pat. No. 6,801,104, WO 2000/060089, WO 2001/026459,WO 2001/035725, WO 2001/034726, WO 2001/035727, WO 2001/036444, WO2001/036597, WO 2001/036598, WO 2002/015675, WO 2002/017430, WO2002/077185, WO 2002/079403, WO 2003/013227, WO 2003/013228, WO2003/014327, WO 2004/031349, WO 2004/076638, WO 98/09521, and WO99/38977 describing genes, including CBF genes and transcription factorseffective in mitigating the negative effects of freezing, high salinity,and drought on plants, as well as conferring other positive effects onplant phenotype; US 2004/0148654 and WO 01/36596 where abscisic acid isaltered in plants resulting in improved plant phenotype such asincreased yield and/or increased tolerance to abiotic stress; WO2000/006341, WO 04/090143, U.S. application Ser. No. 10/817,483 and U.S.Pat. No. 6,992,237 where cytokinin expression is modified resulting inplants with increased stress tolerance, such as drought tolerance,and/or increased yield. Also see WO 02/02776, WO 2003/052063,JP2002281975, U.S. Pat. No. 6,084,153, WO 01/64898, U.S. Pat. Nos.6,177,275 and 6,107,547 (enhancement of nitrogen utilization and alterednitrogen responsiveness). For ethylene alteration, see US 20040128719,US 20030166197 and WO 2000/32761. For plant transcription factors ortranscriptional regulators of abiotic stress, see e.g. US 20040098764 orUS 20040078852.

Other genes and transcription factors that affect plant growth andagronomic traits such as yield, flowering, plant growth and/or plantstructure, can be introduced or introgressed into plants, see e.g. WO97/49811 (LHY), WO 98/56918 (ESD4), WO 97/10339 and U.S. Pat. No.6,573,430 (TFL), U.S. Pat. No. 6,713,663 (FT), WO 96/14414 (CON), WO96/38560, WO 01/21822 (VRN1), WO 00/44918 (VRN2), WO 99/49064 (GI), WO00/46358 (FR1), WO 97/29123, U.S. Pat. No. 6,794,560, U.S. Pat. No.6,307,126 (GAI), WO 99/09174 (D8 and Rht), and WO 2004/076638 and WO2004/031349 (transcription factors).

Methods for Soybean Transformation

Numerous methods for plant transformation have been developed includingbiological and physical plant transformation protocols. See, forexample, Miki et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, Glick,B. R. and Thompson, J. E. Eds. (CRC Press, Inc. Boca Raton, 1993) pages67-88. In addition, expression vectors and in-vitro culture methods forplant cell or tissue transformation and regeneration of plants areavailable. See, for example, Gruber et al., “Vectors for PlantTransformation” in Methods in Plant Molecular Biology and Biotechnology,Glick, B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton,1993) pages 89-119.

A. Agrobacterium-mediated Transformation—One method for introducing anexpression vector into plants is based on the natural transformationsystem of Agrobacterium. See, for example, Horsch et al., Science227:1229 (1985). A. tumefaciens and A. rhizogenes are plant pathogenicsoil bacteria which genetically transform plant cells. The Ti and Riplasmids of A. tumefaciens and A. rhizogenes, respectively, carry genesresponsible for genetic transformation of the plant. See, for example,Kado, C. I., Crit. Rev. Plant Sci. 10:1 (1991). Descriptions ofAgrobacterium vector systems and methods for Agrobacterium-mediated genetransfer are provided by Gruber et al., supra, Miki et al., supra andMoloney et al., Plant Cell Reports 8:238 (1989). See also, U.S. Pat. No.5,563,055 (Townsend and Thomas), issued Oct. 8, 1996.

B. Direct Gene Transfer—Several methods of plant transformation,collectively referred to as direct gene transfer, have been developed asan alternative to Agrobacterium-mediated transformation. A generallyapplicable method of plant transformation is microprojectile-mediatedtransformation where DNA is carried on the surface of microprojectilesmeasuring 1 to 4 μm. The expression vector is introduced into planttissues with a biolistic device that accelerates the microprojectiles tospeeds of 300 to 600 m/s which is sufficient to penetrate plant cellwalls and membranes. Sanford et al., Part. Sci. Technol. 5:27 (1987);Sanford, J. C., Trends Biotech. 6:299 (1988); Klein et al., Bio/Tech.6:559-563 (1988); Sanford, J. C. Physiol Plant 7:206 (1990); Klein etal., Biotechnology 10:268 (1992). See also U.S. Pat. No. 5,015,580(Christou, et al.), issued May 14, 1991 and U.S. Pat. No. 5,322,783(Tomes, et al.), issued Jun. 21, 1994.

Another method for physical delivery of DNA to plants is sonication oftarget cells. Zhang et al., Bio/Technology 9:996 (1991). Alternatively,liposome and spheroplast fusion have been used to introduce expressionvectors into plants. Deshayes et al., EMBO J., 4:2731 (1985); Christouet al., Proc Natl. Acad. Sci. USA 84:3962 (1987). Direct uptake of DNAinto protoplasts using CaCl₂ precipitation, polyvinyl alcohol orpoly-L-ornithine have also been reported. Hain et al., Mol. Gen. Genet.199:161 (1985) and Draper et al., Plant Cell Physiol. 23:451 (1982).Electroporation of protoplasts and whole cells and tissues have alsobeen described (Donn et al., In Abstracts of VIIth InternationalCongress on Plant Cell and Tissue Culture IAPTC, A2-38, p 53 (1990);D'Halluin et al., Plant Cell 4:1495-1505 (1992) and Spencer et al.,Plant Mol. Biol. 24:51-61 (1994)).

Following transformation of soybean target tissues, expression of theabove-described selectable marker genes allows for preferentialselection of transformed cells, tissues and/or plants, usingregeneration and selection methods well known in the art.

The foregoing methods for transformation would typically be used forproducing a transgenic variety. The transgenic variety could then becrossed with another (non-transformed or transformed) variety in orderto produce a new transgenic variety. Alternatively, a genetic trait thathas been engineered into a particular soybean line using the foregoingtransformation techniques could be moved into another line usingtraditional backcrossing techniques that are well known in the plantbreeding arts. For example, a backcrossing approach could be used tomove an engineered trait from a public, non-elite variety into an elitevariety, or from a variety containing a foreign gene in its genome intoa variety or varieties that do not contain that gene. As used herein,“crossing” can refer to a simple X by Y cross or the process ofbackcrossing depending on the context.

Genetic Marker Profile Through SSR and First Generation Progeny

In addition to phenotypic observations, a plant can also be identifiedby its genotype. The genotype of a plant can be characterized through agenetic marker profile which can identify plants of the same variety ora related variety or be used to determine or validate a pedigree.Genetic marker profiles can be obtained by techniques such asRestriction Fragment Length Polymorphisms (RFLPs), Randomly AmplifiedPolymorphic DNAs (RAPDs), Arbitrarily Primed Polymerase Chain Reaction(AP-PCR), DNA Amplification Fingerprinting (DAF), Sequence CharacterizedAmplified Regions (SCARs), Amplified Fragment Length Polymorphisms(AFLPs), Simple Sequence Repeats (SSRs) which are also referred to asMicrosatellites, and Single Nucleotide Polymorphisms (SNPs). Forexample, see Cregan et. al, “An Integrated Genetic Linkage Map of theSoybean Genome” Crop Science 39:1464-1490 (1999), and Berry et al.,Assessing Probability of Ancestry Using Simple Sequence Repeat Profiles:Applications to Maize Inbred Lines and Soybean Varieties” Genetics165:331-342 (2003), each of which are incorporated by reference hereinin their entirety.

Particular markers used for these purposes are not limited to anyparticular set of markers, but are envisioned to include any type ofmarker and marker profile which provides a means of distinguishingvarieties. One method of comparison is to use only homozygous loci for7904162.

Primers and PCR protocols for assaying these and other markers aredisclosed in the Soybase (sponsored by the USDA Agricultural ResearchService and Iowa State University). In addition to being used foridentification of soybean variety 7904162 and plant parts and plantcells of variety 7904162, the genetic profile may be used to identify asoybean plant produced through the use of 7904162 or to verify apedigree for progeny plants produced through the use of 7904162. Thegenetic marker profile is also useful in breeding and developingbackcross conversions.

The present invention comprises a soybean plant characterized bymolecular and physiological data obtained from the representative sampleof said variety deposited with the American Type Culture Collection(ATCC). Further provided by the invention is a soybean plant formed bythe combination of the disclosed soybean plant or plant cell withanother soybean plant or cell and comprising the homozygous alleles ofthe variety.

Means of performing genetic marker profiles using SSR polymorphisms arewell known in the art. SSRs are genetic markers based on polymorphismsin repeated nucleotide sequences, such as microsatellites. A markersystem based on SSRs can be highly informative in linkage analysisrelative to other marker systems in that multiple alleles may bepresent. Another advantage of this type of marker is that, through useof flanking primers, detection of SSRs can be achieved, for example, bythe polymerase chain reaction (PCR), thereby eliminating the need forlabor-intensive Southern hybridization. The PCR detection is done by useof two oligonucleotide primers flanking the polymorphic segment ofrepetitive DNA. Repeated cycles of heat denaturation of the DNA followedby annealing of the primers to their complementary sequences at lowtemperatures, and extension of the annealed primers with DNA polymerase,comprise the major part of the methodology.

Following amplification, markers can be scored by electrophoresis of theamplification products. Scoring of marker genotype is based on the sizeof the amplified fragment, which may be measured by the number of basepairs of the fragment. While variation in the primer used or inlaboratory procedures can affect the reported fragment size, relativevalues should remain constant regardless of the specific primer orlaboratory used. When comparing varieties it is preferable if all SSRprofiles are performed in the same lab.

Primers used are publicly available and may be found in the Soybase orCregan supra. See also, PCT Publication No. WO 99/31964 NucleotidePolymorphisms in Soybean, U.S. Pat. No. 6,162,967 Positional Cloning ofSoybean Cyst Nematode Resistance Genes, and U.S. application Ser. No.09/954,773 Soybean Sudden Death Syndrome Resistant Soybeans and Methodsof Breeding and Identifying Resistant Plants, the disclosure of whichare incorporated herein by reference.

The SSR profile of soybean plant 7904162 can be used to identify plantscomprising 7904162 as a parent, since such plants will comprise the samehomozygous alleles as 7904162. Because the soybean variety isessentially homozygous at all relevant loci, most loci should have onlyone type of allele present. In contrast, a genetic marker profile of anF₁ progeny should be the sum of those parents, e.g., if one parent washomozygous for allele x at a particular locus, and the other parenthomozygous for allele y at that locus, then the F₁ progeny will be xy(heterozygous) at that locus. Subsequent generations of progeny producedby selection and breeding are expected to be of genotype x (homozygous),y (homozygous), or xy (heterozygous) for that locus position. When theF₁ plant is selfed or sibbed for successive filial generations, thelocus should be either x or y for that position.

In addition, plants and plant parts substantially benefiting from theuse of 7904162 in their development, such as 7904162 comprising abackcross conversion, transgene, or genetic sterility factor, may beidentified by having a molecular marker profile with a high percentidentity to 7904162. Such a percent identity might be 95%, 96%, 97%,98%, 99%, 99.5% or 99.9% identical to 7904162.

The SSR profile of 7904162 also can be used to identify essentiallyderived varieties and other progeny varieties developed from the use of7904162, as well as cells and other plant parts thereof. Such plants maybe developed using the markers identified in WO 00/31964, U.S. Pat. No.6,162,967 and U.S. application Ser. No. 09/954,773. Progeny plants andplant parts produced using 7904162 may be identified by having amolecular marker profile of at least 25%, 30%, 35%, 40%, 45%, 50%, 55%,60%, 65%, 70%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or99.5% genetic contribution from soybean variety, as measured by eitherpercent identity or percent similarity. Such progeny may be furthercharacterized as being within a pedigree distance of 7904162, such aswithin 1, 2, 3, 4 or 5 or less cross-pollinations to a soybean plantother than 7904162 or a plant that has 7904162 as a progenitor. Uniquemolecular profiles may be identified with other molecular tools such asSNPs and RFLPs.

While determining the SSR genetic marker profile of the plants describedsupra, several unique SSR profiles may also be identified which did notappear in either parent of such plant. Such unique SSR profiles mayarise during the breeding process from recombination or mutation. Acombination of several unique alleles provides a means of identifying aplant variety, an F₁ progeny produced from such variety, and progenyproduced from such variety.

Single-Gene Conversions

When the term “soybean plant” is used in the context of the presentinvention, this also includes any single gene conversions of thatvariety. The term single gene converted plant as used herein refers tothose soybean plants which are developed by a plant breeding techniquecalled backcrossing wherein essentially all of the desired morphologicaland physiological characteristics of a variety are recovered in additionto the single gene transferred into the variety via the backcrossingtechnique. Backcrossing methods can be used with the present inventionto improve or introduce a characteristic into the variety. The term“backcrossing” as used herein refers to the repeated crossing of ahybrid progeny back to the recurrent parent, i.e., backcrossing 1, 2, 3,4, 5, 6, 7, 8 or more times to the recurrent parent. The parentalsoybean plant that contributes the gene for the desired characteristicis termed the nonrecurrent or donor parent. This terminology refers tothe fact that the nonrecurrent parent is used one time in the backcrossprotocol and therefore does not recur. The parental soybean plant towhich the gene or genes from the nonrecurrent parent are transferred isknown as the recurrent parent as it is used for several rounds in thebackcrossing protocol (Poehlman & Sleper, 1994; Fehr, Principles ofCultivar Development pp. 261-286 (1987)). In a typical backcrossprotocol, the original variety of interest (recurrent parent) is crossedto a second variety (nonrecurrent parent) that carries the single geneof interest to be transferred. The resulting progeny from this cross arethen crossed again to the recurrent parent and the process is repeateduntil a soybean plant is obtained wherein essentially all of the desiredmorphological and physiological characteristics of the recurrent parentare recovered in the converted plant, in addition to the singletransferred gene from the nonrecurrent parent.

The selection of a suitable recurrent parent is an important step for asuccessful backcrossing procedure. The goal of a backcross protocol isto alter or substitute a single trait or characteristic in the originalvariety. To accomplish this, a single gene of the recurrent variety ismodified or substituted with the desired gene from the nonrecurrentparent, while retaining essentially all of the rest of the desiredgenetic, and therefore the desired physiological and morphological,constitution of the original variety. The choice of the particularnonrecurrent parent will depend on the purpose of the backcross; one ofthe major purposes is to add some agronomically important trait to theplant. The exact backcrossing protocol will depend on the characteristicor trait being altered to determine an appropriate testing protocol.Although backcrossing methods are simplified when the characteristicbeing transferred is a dominant allele, a recessive allele may also betransferred. In this instance it may be necessary to introduce a test ofthe progeny to determine if the desired characteristic has beensuccessfully transferred.

Many single gene traits have been identified that are not regularlyselected for in the development of a new variety but that can beimproved by backcrossing techniques. Single gene traits may or may notbe transgenic; examples of these traits include but are not limited to,male sterility, waxy starch, herbicide resistance, resistance forbacterial, fungal, or viral disease, insect resistance, male fertility,enhanced nutritional quality, industrial usage, yield stability andyield enhancement. These genes are generally inherited through thenucleus. Several of these single gene traits are described in U.S. Pat.Nos. 5,959,185; 5,973,234 and 5,977,445; the disclosures of which arespecifically hereby incorporated by reference.

Introduction of a New Trait or Locus into 7904162

Variety 7904162 represents a new base genetic variety into which a newlocus or trait may be introgressed. Direct transformation andbackcrossing represent two important methods that can be used toaccomplish such an introgression. The term backcross conversion andsingle locus conversion are used interchangeably to designate theproduct of a backcrossing program.

Backcross Conversions of 7904162

A backcross conversion of 7904162 occurs when DNA sequences areintroduced through backcrossing (Hallauer et al, 1988, “Corn Breeding”Corn and Corn Improvements, No. 18, pp. 463-481), with 7904162 utilizedas the recurrent parent. Both naturally occurring and transgenic DNAsequences may be introduced through backcrossing techniques. A backcrossconversion may produce a plant with a trait or locus conversion in atleast two or more backcrosses, including at least 2 crosses, at least 3crosses, at least 4 crosses, at least 5 crosses and the like. Molecularmarker assisted breeding or selection may be utilized to reduce thenumber of backcrosses necessary to achieve the backcross conversion. Forexample, see Openshaw, S. J. et al., Marker-assisted Selection inBackcross Breeding. In: Proceedings Symposium of the Analysis ofMolecular Data, August 1994, Crop Science Society of America, Corvallis,Oreg., where it is demonstrated that a backcross conversion can be madein as few as two backcrosses.

The complexity of the backcross conversion method depends on the type oftrait being transferred (single genes or closely linked genes as vs.unlinked genes), the level of expression of the trait, the type ofinheritance (cytoplasmic or nuclear) and the types of parents includedin the cross. It is understood by those of ordinary skill in the artthat for single gene traits that are relatively easy to classify, thebackcross method is effective and relatively easy to manage. (SeeHallauer et al. in Corn and Corn Improvement, Sprague and Dudley, ThirdEd. 1998). Desired traits that may be transferred through backcrossconversion include, but are not limited to, sterility (nuclear andcytoplasmic), fertility restoration, nutritional enhancements, droughttolerance, nitrogen utilization, altered fatty acid profile, lowphytate, industrial enhancements, disease resistance (bacterial, fungalor viral), insect resistance and herbicide resistance. In addition, anintrogression site itself, such as an FRT site, Lox site or other sitespecific integration site, may be inserted by backcrossing and utilizedfor direct insertion of one or more genes of interest into a specificplant variety. In some embodiments of the invention, the number of locithat may be backcrossed into 7904162 is at least 1, 2, 3, 4, or 5 and/orno more than 6, 5, 4, 3, or 2. A single locus may contain severaltransgenes, such as a transgene for disease resistance that, in the sameexpression vector, also contains a transgene for herbicide resistance.The gene for herbicide resistance may be used as a selectable markerand/or as a phenotypic trait. A single locus conversion of site specificintegration system allows for the integration of multiple genes at theconverted loci.

The backcross conversion may result from either the transfer of adominant allele or a recessive allele. Selection of progeny containingthe trait of interest is accomplished by direct selection for a traitassociated with a dominant allele. Transgenes transferred viabackcrossing typically function as a dominant single gene trait and arerelatively easy to classify. Selection of progeny for a trait that istransferred via a recessive allele requires growing and selfing thefirst backcross generation to determine which plants carry the recessivealleles. Recessive traits may require additional progeny testing insuccessive backcross generations to determine the presence of the locusof interest. The last backcross generation is usually selfed to givepure breeding progeny for the gene(s) being transferred, although abackcross conversion with a stably introgressed trait may also bemaintained by further backcrossing to the recurrent parent withselection for the converted trait.

Along with selection for the trait of interest, progeny are selected forthe phenotype of the recurrent parent. The backcross is a form ofinbreeding, and the features of the recurrent parent are automaticallyrecovered after successive backcrosses. Poehlman, Breeding Field Crops,P. 204 (1987). Poehlman suggests from one to four or more backcrosses,but as noted above, the number of backcrosses necessary can be reducedwith the use of molecular markers. Other factors, such as a geneticallysimilar donor parent, may also reduce the number of backcrossesnecessary. As noted by Poehlman, backcrossing is easiest for simplyinherited, dominant and easily recognized traits.

One process for adding or modifying a trait or locus in soybean variety7904162 comprises crossing 7904162 plants grown from 7904162 seed withplants of another soybean variety that comprise the desired trait orlocus, selecting F₁ progeny plants that comprise the desired trait orlocus to produce selected F₁ progeny plants, crossing the selectedprogeny plants with the 7904162 plants to produce backcross progenyplants, selecting for backcross progeny plants that have the desiredtrait or locus and the morphological characteristics of soybean variety7904162 to produce selected backcross progeny plants; and backcrossingto 7904162 three or more times in succession to produce selected fourthor higher backcross progeny plants that comprise said trait or locus.The modified 7904162 may be further characterized as having thephysiological and morphological characteristics of soybean variety7904162 listed in Table 1 as determined at the 5% significance levelwhen grown in the same environmental conditions and/or may becharacterized by percent similarity or identity to 7904162 as determinedby SSR markers. The above method may be utilized with fewer backcrossesin appropriate situations, such as when the donor parent is highlyrelated or markers are used in the selection step. Desired traits thatmay be used include those nucleic acids known in the art, some of whichare listed herein, that will affect traits through nucleic acidexpression or inhibition. Desired loci include the introgression of FRT,Lox and other sites for site specific integration, which may also affecta desired trait if a functional nucleic acid is inserted at theintegration site.

In addition, the above process and other similar processes describedherein may be used to produce first generation progeny soybean seed byadding a step at the end of the process that comprises crossing 7904162with the introgressed trait or locus with a different soybean plant andharvesting the resultant first generation progeny soybean seed.

Tissue Culture

Further reproduction of the variety can occur by tissue culture andregeneration. Tissue culture of various tissues of soybeans andregeneration of plants therefrom is well known and widely published. Forexample, reference may be had to Komatsuda, T. et al., Crop Sci.31:333-337 (1991); Stephens, P. A., et al., Theor. Appl. Genet. (1991)82:633-635; Komatsuda, T. et al., Plant Cell, Tissue and Organ Culture,28:103-113 (1992); Dhir, S. et al., Plant Cell Reports (1992)11:285-289; Pandey, P. et al., Japan J. Breed. 42:1-5 (1992); andShetty, K., et al., Plant Science 81:245-251 (1992); as well as U.S.Pat. No. 5,024,944 issued Jun. 18, 1991 to Collins et al., and U.S. Pat.No. 5,008,200 issued Apr. 16, 1991 to Ranch et al. Thus, another aspectof this invention is to provide cells which upon growth anddifferentiation produce soybean plants having the physiological andmorphological characteristics of soybean cultivar 7904162.

As used herein, the term “tissue culture” indicates a compositioncomprising isolated cells of the same or a different type or acollection of such cells organized into parts of a plant. Exemplarytypes of tissue cultures are protoplasts, calli, plant clumps, and plantcells that can generate tissue culture that are intact in plants orparts of plants, such as embryos, pollen, flowers, seeds, pods,petioles, leaves, stems, roots, root tips, anthers, pistils and thelike. Means for preparing and maintaining plant tissue culture are wellknown in the art. By way of example, a tissue culture comprising organshas been used to produce regenerated plants. U.S. Pat. Nos. 5,959,185;5,973,234 and 5,977,445 describe certain techniques, the disclosures ofwhich are incorporated herein by reference.

Using 7904162 to Develop Other Soybean Varieties

Soybean varieties such as 7904162 are typically developed for use inseed and grain production. However, soybean varieties such as 7904162also provide a source of breeding material that may be used to developnew soybean varieties. Plant breeding techniques known in the art andused in a soybean plant breeding program include, but are not limitedto, recurrent selection, mass selection, bulk selection, mass selection,backcrossing, pedigree breeding, open pollination breeding, restrictionfragment length polymorphism enhanced selection, genetic marker enhancedselection, making double haploids, and transformation. Oftencombinations of these techniques are used. The development of soybeanvarieties in a plant breeding program requires, in general, thedevelopment and evaluation of homozygous varieties. There are manyanalytical methods available to evaluate a new variety. The oldest andmost traditional method of analysis is the observation of phenotypictraits but genotypic analysis may also be used.

Additional Breeding Methods

This invention is directed to methods for producing a soybean plant bycrossing a first parent soybean plant with a second parent soybean plantwherein either the first or second parent soybean plant is variety7904162. The other parent may be any other soybean plant, such as asoybean plant that is part of a synthetic or natural population. Anysuch methods using soybean variety 7904162 are part of this invention:selfing, sibbing, backcrosses, mass selection, pedigree breeding, bulkselection, hybrid production, crosses to populations, and the like.These methods are well known in the art and some of the more commonlyused breeding methods are described below. Descriptions of breedingmethods can be found in one of several reference books (e.g., Allard,Principles of Plant Breeding, 1960; Simmonds, Principles of CropImprovement, 1979; Sneep et al., 1979; Fehr, “Breeding Methods forCultivar Development”, Chapter 7, Soybean Improvement, Production andUses, 2.sup.nd ed., Wilcox editor, 1987).

The following describes breeding methods that may be used with soybeancultivar 7904162 in the development of further soybean plants. One suchembodiment is a method for developing a cultivar 7904162 progeny soybeanplant in a soybean plant breeding program comprising: obtaining thesoybean plant, or a part thereof, of cultivar 7904162 utilizing saidplant or plant part as a source of breeding material and selecting asoybean cultivar 7904162 progeny plant with molecular markers in commonwith cultivar 7904162 and/or with morphological and/or physiologicalcharacteristics selected from the characteristics listed in Tables 1 or2. Breeding steps that may be used in the soybean plant breeding programinclude pedigree breeding, backcrossing, mutation breeding, andrecurrent selection. In conjunction with these steps, techniques such asRFLP-enhanced selection, genetic marker enhanced selection (for exampleSSR markers) and the making of double haploids may be utilized.

Another method involves producing a population of soybean cultivar7904162 progeny soybean plants, comprising crossing cultivar 7904162with another soybean plant, thereby producing a population of soybeanplants, which, on average, derive 50% of their alleles from soybeancultivar 7904162. A plant of this population may be selected andrepeatedly selfed or sibbed with a soybean cultivar resulting from thesesuccessive filial generations. One embodiment of this invention is thesoybean cultivar produced by this method and that has obtained at least50% of its alleles from soybean cultivar 7904162.

One of ordinary skill in the art of plant breeding would know how toevaluate the traits of two plant varieties to determine if there is nosignificant difference between the two traits expressed by thosevarieties. For example, see Fehr and Walt, Principles of CultivarDevelopment, p 261-286 (1987). Thus the invention includes soybeancultivar 7904162 progeny soybean plants comprising a combination of atleast two cultivar 7904162 traits selected from the group consisting ofthose listed in Tables 1 and 2 or the cultivar 7904162 combination oftraits listed in the Summary of the Invention, so that said progenysoybean plant is not significantly different for said traits thansoybean cultivar 7904162 as determined at the 5% significance level whengrown in the same environmental conditions. Using techniques describedherein, molecular markers may be used to identify said progeny plant asa soybean cultivar 7904162 progeny plant. Mean trait values may be usedto determine whether trait differences are significant, and preferablythe traits are measured on plants grown under the same environmentalconditions. Once such a variety is developed its value is substantialsince it is important to advance the germplasm base as a whole in orderto maintain or improve traits such as yield, disease resistance, pestresistance, and plant performance in extreme environmental conditions.

Progeny of soybean cultivar 7904162 may also be characterized throughtheir filial relationship with soybean cultivar 7904162, as for example,being within a certain number of breeding crosses of soybean cultivar7904162. A breeding cross is a cross made to introduce new genetics intothe progeny, and is distinguished from a cross, such as a self or a sibcross, made to select among existing genetic alleles. The lower thenumber of breeding crosses in the pedigree, the closer the relationshipbetween soybean cultivar 7904162 and its progeny. For example, progenyproduced by the methods described herein may be within 1, 2, 3, 4 or 5breeding crosses of soybean cultivar 7904162.

As used herein, the term “plant” includes plant cells, plantprotoplasts, plant cell tissue cultures from which soybean plants can beregenerated, plant calli, plant clumps, and plant cells that are intactin plants or parts of plants, such as embryos, pollen, ovules, flowers,pods, leaves, roots, root tips, anthers, cotyledons, hypocotyls,meristematic cells, stems, pistils, petiole, and the like.

Pedigree Breeding

Pedigree breeding starts with the crossing of two genotypes, such as7904162 and another soybean variety having one or more desirablecharacteristics that is lacking or which complements 7904162. If the twooriginal parents do not provide all the desired characteristics, othersources can be included in the breeding population. In the pedigreemethod, superior plants are selfed and selected in successive filialgenerations. In the succeeding filial generations the heterozygouscondition gives way to homogeneous varieties as a result ofself-pollination and selection. Typically in the pedigree method ofbreeding, five or more successive filial generations of selfing andselection is practiced: F₁ to F₂; F₂ to F₃; F₃ to F₄; F₄ to F₅, etc.After a sufficient amount of inbreeding, successive filial generationswill serve to increase seed of the developed variety. Preferably, thedeveloped variety comprises homozygous alleles at about 95% or more ofits loci.

In addition to being used to create a backcross conversion, backcrossingcan also be used in combination with pedigree breeding. As discussedpreviously, backcrossing can be used to transfer one or morespecifically desirable traits from one variety, the donor parent, to adeveloped variety called the recurrent parent, which has overall goodagronomic characteristics yet lacks that desirable trait or traits.However, the same procedure can be used to move the progeny toward thegenotype of the recurrent parent but at the same time retain manycomponents of the non-recurrent parent by stopping the backcrossing atan early stage and proceeding with selfing and selection. For example, asoybean variety may be crossed with another variety to produce a firstgeneration progeny plant. The first generation progeny plant may then bebackcrossed to one of its parent varieties to create a BC1 or BC2.Progeny are selfed and selected so that the newly developed variety hasmany of the attributes of the recurrent parent and yet several of thedesired attributes of the non-recurrent parent. This approach leveragesthe value and strengths of the recurrent parent for use in new soybeanvarieties.

Therefore, an embodiment of this invention is a method of making abackcross conversion of soybean variety 7904162, comprising the steps ofcrossing a plant of soybean variety 7904162 with a donor plantcomprising a desired trait, selecting an F₁ progeny plant comprising thedesired trait, and backcrossing the selected F₁ progeny plant to a plantof soybean variety 7904162. This method may further comprise the step ofobtaining a molecular marker profile of soybean variety 7904162 andusing the molecular marker profile to select for a progeny plant withthe desired trait and the molecular marker profile of 7904162. In oneembodiment the desired trait is a mutant gene or transgene present inthe donor parent.

Recurrent Selection and Mass Selection

Recurrent selection is a method used in a plant breeding program toimprove a population of plants. 7904162 is suitable for use in arecurrent selection program. The method entails individual plants crosspollinating with each other to form progeny. The progeny are grown andthe superior progeny selected by any number of selection methods, whichinclude individual plant, half-sib progeny, full-sib progeny and selfedprogeny. The selected progeny are cross pollinated with each other toform progeny for another population. This population is planted andagain superior plants are selected to cross pollinate with each other.Recurrent selection is a cyclical process and therefore can be repeatedas many times as desired. The objective of recurrent selection is toimprove the traits of a population. The improved population can then beused as a source of breeding material to obtain new varieties forcommercial or breeding use, including the production of a syntheticcultivar. A synthetic cultivar is the resultant progeny formed by theintercrossing of several selected varieties.

Mass selection is a useful technique when used in conjunction withmolecular marker enhanced selection. In mass selection seeds fromindividuals are selected based on phenotype or genotype. These selectedseeds are then bulked and used to grow the next generation. Bulkselection requires growing a population of plants in a bulk plot,allowing the plants to self-pollinate, harvesting the seed in bulk andthen using a sample of the seed harvested in bulk to plant the nextgeneration. Also, instead of self pollination, directed pollinationcould be used as part of the breeding program.

Mutation Breeding

Mutation breeding is another method of introducing new traits intosoybean variety 7904162. Mutations that occur spontaneously or areartificially induced can be useful sources of variability for a plantbreeder. The goal of artificial mutagenesis is to increase the rate ofmutation for a desired characteristic. Mutation rates can be increasedby many different means including temperature, long-term seed storage,tissue culture conditions, radiation; such as X-rays, Gamma rays (e.g.cobalt 60 or cesium 137), neutrons, (product of nuclear fission byuranium 235 in an atomic reactor), Beta radiation (emitted fromradioisotopes such as phosphorus 32 or carbon 14), or ultravioletradiation (preferably from 2500 to 2900 nm), or chemical mutagens (suchas base analogues (5-bromo-uracil), related compounds (8-ethoxycaffeine), antibiotics (streptonigrin), alkylating agents (sulfurmustards, nitrogen mustards, epoxides, ethylenamines, sulfates,sulfonates, sulfones, lactones), azide, hydroxylamine, nitrous acid, oracridines. Once a desired trait is observed through mutagenesis thetrait may then be incorporated into existing germplasm by traditionalbreeding techniques. Details of mutation breeding can be found in“Principles of Cultivar Development” Fehr, 1993 Macmillan PublishingCompany. In addition, mutations created in other soybean plants may beused to produce a backcross conversion of soybean cultivar 7904162 thatcomprises such mutation.

Breeding with Molecular Markers

Molecular markers, which includes markers identified through the use oftechniques such as Isozyme Electrophoresis, Restriction Fragment LengthPolymorphisms (RFLPs), Randomly Amplified Polymorphic DNAs (RAPDs),Arbitrarily Primed Polymerase Chain Reaction (AP-PCR), DNA AmplificationFingerprinting (DAF), Sequence Characterized Amplified Regions (SCARs),Amplified Fragment Length Polymorphisms (AFLPs), Simple Sequence Repeats(SSRs) and Single Nucleotide Polymorphisms (SNPs), may be used in plantbreeding methods utilizing soybean cultivar 7904162.

Isozyme Electrophoresis and RFLPs have been widely used to determinegenetic composition. Shoemaker and Olsen, ((1993) Molecular Linkage Mapof Soybean (Glycine max L. Merr.). p. 6.131-6.138. In S. J. O'Brien(ed.) Genetic Maps: Locus Maps of Complex Genomes. Cold Spring HarborLaboratory Press. Cold Spring Harbor, N.Y.), developed a moleculargenetic linkage map that consisted of 25 linkage groups with about 365RFLP, 11 RAPD (random amplified polymorphic DNA), three classicalmarkers, and four isozyme loci. See also, Shoemaker R. C. 1994 RFLP Mapof Soybean. P. 299-309 In R. L. Phillips and I. K. Vasil (ed.) DNA-basedmarkers in plants. Kluwer Academic Press Dordrecht, the Netherlands.

SSR technology is currently the most efficient and practical markertechnology; more marker loci can be routinely used and more alleles permarker locus can be found using SSRs in comparison to RFLPs. For exampleDiwan and Cregan, described a highly polymorphic microsatellite loci insoybean with as many as 26 alleles. (Diwan, N., and P. B. Cregan 1997Automated sizing of fluorescent-labeled simple sequence repeat (SSR)markers to assay genetic variation in Soybean Theor. Appl. Genet.95:220-225.) Single Nucleotide Polymorphisms may also be used toidentify the unique genetic composition of the invention and progenyvarieties retaining that unique genetic composition. Various molecularmarker techniques may be used in combination to enhance overallresolution.

Soybean DNA molecular marker linkage maps have been rapidly constructedand widely implemented in genetic studies. One such study is describedin Cregan et. al, “An Integrated Genetic Linkage Map of the SoybeanGenome” Crop Science 39:1464-1490 (1999). Sequences and PCR conditionsof SSR Loci in Soybean as well as the most current genetic map may befound in Soybase on the world wide web.

One use of molecular markers is Quantitative Trait Loci (QTL) mapping.QTL mapping is the use of markers, which are known to be closely linkedto alleles that have measurable effects on a quantitative trait.Selection in the breeding process is based upon the accumulation ofmarkers linked to the positive effecting alleles and/or the eliminationof the markers linked to the negative effecting alleles from the plant'sgenome.

Molecular markers can also be used during the breeding process for theselection of qualitative traits. For example, markers closely linked toalleles or markers containing sequences within the actual alleles ofinterest can be used to select plants that contain the alleles ofinterest during a backcrossing breeding program. The markers can also beused to select for the genome of the recurrent parent and against thegenome of the donor parent. Using this procedure can minimize the amountof genome from the donor parent that remains in the selected plants. Itcan also be used to reduce the number of crosses back to the recurrentparent needed in a backcrossing program. The use of molecular markers inthe selection process is often called genetic marker enhanced selection.Molecular markers may also be used to identify and exclude certainsources of germplasm as parental varieties or ancestors of a plant byproviding a means of tracking genetic profiles through crosses.

Production of Double Haploids

The production of double haploids can also be used for the developmentof plants with a homozygous phenotype in the breeding program. Forexample, a soybean plant for which soybean cultivar 7904162 is a parentcan be used to produce double haploid plants. Double haploids areproduced by the doubling of a set of chromosomes (1 N) from aheterozygous plant to produce a completely homozygous individual. Forexample, see Wan et al., “Efficient Production of Doubled Haploid PlantsThrough Colchicine Treatment of Anther-Derived Maize Callus”,Theoretical and Applied Genetics, 77:889-892, 1989 and U.S. Pat. No.7,135,615. This can be advantageous because the process omits thegenerations of selfing needed to obtain a homozygous plant from aheterozygous source.

Haploid induction systems have been developed for various plants toproduce haploid tissues, plants and seeds. The haploid induction systemcan produce haploid plants from any genotype by crossing a selected line(as female) with an inducer line. Such inducer lines for maize includeStock 6 (Coe, 1959, Am. Nat. 93:381-382; Sharkar and Coe, 1966, Genetics54:453-464), KEMS (Deimling, Roeber, and Geiger, 1997, Vortr.Pflanzenzuchtg 38:203-224), or KMS and ZMS (Chalyk, Bylich & Chebotar,1994, MNL 68:47; Chalyk & Chebotar, 2000, Plant Breeding 119:363-364),and indeterminate gametophyte (ig) mutation (Kermicle 1969 Science166:1422-1424). The disclosures of which are incorporated herein byreference.

Methods for obtaining haploid plants are also disclosed in Kobayashi, M.et al., Journ. of Heredity 71(1):9-14, 1980, Pollacsek, M., Agronomie(Paris) 12(3):247-251, 1992; Cho-Un-Haing et al., Journ. of Plant Biol.,1996, 39(3):185-188; Verdoodt, L., et al., February 1998, 96(2):294-300;Genetic Manipulation in Plant Breeding, Proceedings InternationalSymposium Organized by EUCARPIA, Sep. 8-13, 1985, Berlin, Germany;Chalyk et al., 1994, Maize Genet Coop. Newsletter 68:47; Chalyk, S.

Thus, an embodiment of this invention is a process for making asubstantially homozygous 7904162 progeny plant by producing or obtaininga seed from the cross of 7904162 and another soybean plant and applyingdouble haploid methods to the F₁ seed or F₁ plant or to any successivefilial generation. Based on studies in maize and currently beingconducted in soybean, such methods would decrease the number ofgenerations required to produce a variety with similar genetics orcharacteristics to 7904162. See Bernardo, R. and Kahler, A. L., Theor.Appl. Genet. 102:986-992, 2001.

In particular, a process of making seed retaining the molecular markerprofile of soybean variety 7904162 is contemplated, such processcomprising obtaining or producing F₁ seed for which soybean variety7904162 is a parent, inducing doubled haploids to create progeny withoutthe occurrence of meiotic segregation, obtaining the molecular markerprofile of soybean variety 7904162, and selecting progeny that retainthe molecular marker profile of 7904162.

Descriptions of other breeding methods that are commonly used fordifferent traits and crops can be found in one of several referencebooks (e.g., Allard, 1960; Simmonds, 1979; Sneep et al., 1979; Fehr,1987).

INDUSTRIAL USES

The seed of soybean cultivar 7904162, the plant produced from the seed,the hybrid soybean plant produced from the crossing of the variety withany other soybean plant, hybrid seed, and various parts of the hybridsoybean plant can be utilized for human food, livestock feed, and as araw material in industry. The soybean seed can be crushed or a componentof the soybean seed can be extracted in order to comprise a componentfor a food or feed product.

The soybean is the world's leading source of vegetable oil and proteinmeal. The oil extracted from soybeans is used for cooking oil,margarine, and salad dressings. Soybean oil is composed of saturated,monounsaturated and polyunsaturated fatty acids. It has a typicalcomposition of 11% palmitic, 4% stearic, 25% oleic, 50% linoleic and 9%linolenic fatty acid content (“Economic Implications of Modified SoybeanTraits Summary Report”, Iowa Soybean Promotion Board and AmericanSoybean Association Special Report 92S, May 1990). Changes in fatty acidcomposition for improved oxidative stability and nutrition areconstantly sought after. Industrial uses of soybean oil which issubjected to further processing include ingredients for paints,plastics, fibers, detergents, cosmetics, lubricants and biodiesel fuel.Soybean oil may be split, inter-esterified, sulfurized, epoxidized,polymerized, ethoxylated, or cleaved. Designing and producing soybeanoil derivatives with improved functionality and improved oliochemistryis a rapidly growing field. The typical mixture of triglycerides isusually split and separated into pure fatty acids, which are thencombined with petroleum-derived alcohols or acids, nitrogen, sulfonates,chlorine, or with fatty alcohols derived from fats and oils.

Soybean is also used as a food source for both animals and humans.Soybean is widely used as a source of protein for animal feeds forpoultry, swine and cattle. During processing of whole soybeans, thefibrous hull is removed and the oil is extracted. The remaining soybeanmeal is a combination of carbohydrates and approximately 50% protein.

For human consumption soybean meal is made into soybean flour which isprocessed to protein concentrates used for meat extenders or specialtypet foods. Production of edible protein ingredients from soybean offersa healthier, less expensive replacement for animal protein in meats aswell as in dairy-type products.

Tables

In Table 2 that follows, the traits and characteristics of soybeancultivar 7904162 are compared to several competing varieties ofcommercial soybeans of similar maturity. In Table 2, column 1 shows thecomparison number, column 2 shows the test year, column 3 shows thenumber of locations, column 4 shows the number of observations, column 5indicates the genotype, column 6 shows the mean yield, column 7indicates the t value and columns 8 and 9 indicate the critical t valuesat the 0.05% and 0.01% levels of significance, respectively.

As shown in Table 2, soybean cultivar 7904162 yields better than 20commercial varieties with the increase over 13 varieties beingsignificant at the 0.01 level of probability and the increase over 4varieties being significant at the 0.05 level of probability.

TABLE 2 PAIRED COMPARISONS # of # of t Critical Critical Comp # YearLoc. Obs Genotype Mean Yield Value t @ .05 t @ .01 1 2007 20 39 790416247.6 1.48 1.69 2.43 CSR1000 46.3 2 2007 20 39 7904162 47.6 2.34* 1.692.43 CSR1320 45.4 3 2007 20 39 7904162 47.6 2.80** 1.69 2.43 NKS12-P445.3 4 2007 20 39 7904162 47.6 2.67** 1.69 2.43 CSR1510 45.0 5 2007 2039 7904162 47.6 2.57** 1.69 2.43 CSR1533 45.5 6 2007 20 39 7904162 47.62.39* 1.69 2.43 CSR2114 45.7 7 2007 20 39 7904162 47.6 5.42** 1.69 2.43P91M30 43.5 8 2007 20 39 7904162 47.6 3.48** 1.69 2.43 CSR1410 44.6 92007 20 39 7904162 47.6 1.43 1.69 2.43 CSR1422N 46.3 10 2007 20 397904162 47.6 1.87* 1.69 2.43 CSR1522N 46.1 11 2007 20 39 7904162 47.61.62 1.69 2.43 ASI146 46.0 12 2007 20 39 7904162 47.6 3.76** 1.69 2.43CSR1412N 44.3 13 2007 20 39 7904162 47.6 5.14** 1.69 2.43 JG913034RJ43.4 14 2007 20 39 7904162 47.6 1.90* 1.69 2.43 JG915034 46.0 15 2007 2039 7904162 47.6 4.94** 1.69 2.43 NKS14-A7 43.4 16 2007 20 39 790416247.6 4.47** 1.69 2.43 NKS15-E3 44.0 17 2007 20 39 7904162 47.6 2.99**1.69 2.43 SG1570NRR 45.0 18 2007 20 39 7904162 47.6 2.53** 1.69 2.43NKS17-P9 45.1 19 2007 20 39 7904162 47.6 4.87** 1.69 2.43 P91M61 43.2 202007 20 39 7904162 47.6 2.99** 1.69 2.43 P91M91 45.2 *Significant at .05level of probability **Significant at .01 level of probability

Deposit Information

A deposit of the soybean seed of this invention is maintained by StineSeed Farm, Inc., 22555 Laredo Trail, AdeI, Iowa 50003. Access to thisdeposit will be available during the pendency of this application topersons determined by the Commissioner of Patents and Trademarks to beentitled thereto under 37 CFR §1.14 and 35 USC §122. Upon allowance ofany claims in this application, all restrictions on the availability tothe public of the variety will be irrevocably removed by affordingaccess to a deposit of at least 2,500 seeds of the same variety with theAmerican Type Culture Collection, Manassas, Va. or National Collectionsof Industrial, Food and Marine Bacteria (NCIMB), 23 St Machar Drive,Aberdeen, Scotland, AB24 3RY, United Kingdom.

While a number of exemplary aspects and embodiments have been discussedabove, those of skill in the art will recognize certain modifications,permutations, additions and sub-combinations thereof. It is thereforeintended that the following appended claims and claims hereafterintroduced are interpreted to include all such modifications,permutations, additions and sub-combinations as are within their truespirit and scope.

1. A seed of soybean cultivar 7904162, representative sample seed of said cultivar was deposited under ATCC Accession No. PTA-______.
 2. A soybean plant, or a part thereof, produced by growing the seed of claim
 1. 3. A tissue culture produced from protoplasts or cells from the plant of claim 2, wherein said cells or protoplasts of the tissue culture are produced from a plant part selected from the group consisting of leaf, pollen, embryo, cotyledon, hypocotyl, meristematic cell, root, root tip, pistil, anther, flower, shoot, stem, pod and petiole.
 4. A soybean plant regenerated from the tissue culture of claim 3, wherein the plant has all of the morphological and physiological characteristics of cultivar
 7904162. 5. A method for producing a soybean seed comprising crossing two soybean plants and harvesting the resultant soybean seed, wherein at least one soybean plant is the soybean plant of claim
 2. 6. A soybean seed produced by the method of claim
 5. 7. A soybean plant, or a part thereof, produced by growing said seed of claim
 6. 8. A method of producing an herbicide resistant soybean plant wherein the method comprises transforming the soybean plant of claim 2 with a transgene wherein the transgene confers resistance to an herbicide selected from the group consisting of imidazolinone, cyclohexanedione, sulfonylurea, glyphosate, glufosinate, phenoxy proprionic acid, L-phosphinothricin, triazine and benzonitrile.
 9. An herbicide resistant soybean plant produced by the method of claim
 8. 10. A method of producing a pest or insect resistant soybean plant wherein the method comprises transforming the soybean plant of claim 2 with a transgene that confers pest or insect resistance.
 11. A pest or insect resistant soybean plant produced by the method of claim
 10. 12. The soybean plant of claim 11, wherein the transgene encodes a Bacillus thuringiensis endotoxin.
 13. A method of producing a disease resistant soybean plant wherein the method comprises transforming the soybean plant of claim 2 with a transgene that confers disease resistance.
 14. A disease resistant soybean plant produced by the method of claim
 13. 15. A method of producing a soybean plant with modified fatty acid metabolism or modified carbohydrate metabolism wherein the method comprises transforming the soybean plant of claim 2 with a transgene encoding a protein selected from the group consisting of phytase, fructosyltransferase, levansucrase, α-amylase, invertase and starch branching enzyme or encoding an antisense of stearyl-ACP desaturase.
 16. A soybean plant having modified fatty acid metabolism or modified carbohydrate metabolism produced by the method of claim
 15. 17. A method of introducing a desired trait into soybean cultivar 7904162 wherein the method comprises: (a) crossing a 7904162 plant, wherein a representative sample of seed was deposited under ATCC Accession No. PTA-______, with a plant of another soybean cultivar that comprises a desired trait to produce progeny plants wherein the desired trait is selected from the group consisting of male sterility, herbicide resistance, insect resistance, modified fatty acid metabolism, modified carbohydrate metabolism, modified seed yield, modified oil percent, modified protein percent, modified lodging resistance, modified shattering, modified iron-deficiency chlorosis and resistance to bacterial disease, fungal disease or viral disease; (b) selecting one or more progeny plants that have the desired trait to produce selected progeny plants; (c) crossing the selected progeny plants with the 7904162 plants to produce backcross progeny plants; (d) selecting for backcross progeny plants that have the desired trait and all of the physiological and morphological characteristics of soybean cultivar 7904162 listed in Table 1; and (e) repeating steps (c) and (d) three or more times in succession to produce selected fourth or higher backcross progeny plants that comprise the desired trait and all of the physiological and morphological characteristics of soybean cultivar 7904162 listed in Table
 1. 18. A soybean plant produced by the method of claim 17, wherein the plant has the desired trait.
 19. The soybean plant of claim 18, wherein the desired trait is herbicide resistance and the resistance is conferred to an herbicide selected from the group consisting of imidazolinone, cyclohexanedione, sulfonylurea, glyphosate, glufosinate, phenoxy proprionic acid, L-phosphinothricin, triazine and benzonitrile.
 20. The soybean plant of claim 18, wherein the desired trait is insect resistance and the insect resistance is conferred by a transgene encoding a Bacillus thuringiensis endotoxin.
 21. The soybean plant of claim 18, wherein the desired trait is modified fatty acid metabolism or modified carbohydrate metabolism and said desired trait is conferred by a nucleic acid encoding a protein selected from the group consisting of phytase, fructosyltransferase, levansucrase, α-amylase, invertase and starch branching enzyme or encoding an antisense of stearyl-ACP desaturase.
 22. A food or feed product comprising a component from the seed of claim 1 following crushing or extraction. 